[med-svn] [partitionfinder] 01/06: Imported Upstream version 2.0.0-pre9
Kevin Murray
daube-guest at moszumanska.debian.org
Tue Nov 10 10:05:04 UTC 2015
This is an automated email from the git hooks/post-receive script.
daube-guest pushed a commit to branch master
in repository partitionfinder.
commit aed3813e0619361cd689acbe309a39953431d345
Author: Kevin Murray <spam at kdmurray.id.au>
Date: Tue Nov 10 17:30:26 2015 +1100
Imported Upstream version 2.0.0-pre9
---
.gitignore | 56 +
.gitmodules | 8 +
PartitionFinder.py | 23 +
PartitionFinderProtein.py | 23 +
README.md | 38 +
all_tests.sh | 1 +
build_ext.py | 33 +
build_programs.sh | 30 +
clean_tests.sh | 2 +
docs/Figure1.pptx | Bin 0 -> 131102 bytes
docs/Manual_v1.0.0.pdf | Bin 0 -> 742350 bytes
docs/Manual_v1.0.1.pdf | Bin 0 -> 740913 bytes
docs/Manual_v1.1.1.pdf | Bin 0 -> 734381 bytes
docs/Manual_v2.0.0.docx | Bin 0 -> 385328 bytes
docs/Manual_v2.0.0.pdf | Bin 0 -> 737510 bytes
docs/PartitionFinder_Manual_v1.0.1.docx | Bin 0 -> 645022 bytes
docs/PartitionFinder_Manual_v1.1.0.docx | Bin 0 -> 390084 bytes
docs/README.md | 119 +
docs/citationsplot.pdf | Bin 0 -> 5148 bytes
docs/citationsplot2.pdf | Bin 0 -> 5690 bytes
docs/downloadplot.pdf | Bin 0 -> 5710 bytes
docs/downloadplot.r | 64 +
docs/downloadstats.csv | 1 +
docs/evoldir_annoucement_1.txt | 29 +
docs/evoldir_annoucement_2.txt | 41 +
docs/googlegroup_analysis.r | 10 +
docs/googlegroup_stats.csv | 1 +
docs/tiger_compilation.txt | 51 +
examples/README.txt | 18 +
examples/aminoacid/Als_etal_2004.phy | 5 +
examples/aminoacid/partition_finder.cfg | 23 +
examples/kmeans/partition_finder.cfg | 19 +
examples/kmeans/test.phy | 11 +
examples/nucleotide/partition_finder.cfg | 29 +
examples/nucleotide/test.phy | 5 +
partfinder/__init__.py | 16 +
partfinder/_tiger.cpp | 20553 +++++++++++++++++++
partfinder/_tiger.pxd | 40 +
partfinder/_tiger.pyx | 125 +
partfinder/algorithm.py | 106 +
partfinder/alignment.py | 442 +
partfinder/analysis.py | 295 +
partfinder/analysis_method.py | 830 +
partfinder/config.py | 478 +
partfinder/database.py | 168 +
partfinder/entropy.py | 101 +
partfinder/kmeans.py | 175 +
partfinder/logtools.py | 160 +
partfinder/main.py | 429 +
partfinder/model_loader.py | 181 +
partfinder/model_utils.py | 65 +
partfinder/models.csv | 1 +
partfinder/neighbour.py | 287 +
partfinder/parser.py | 310 +
partfinder/phyml.py | 226 +
partfinder/phyml_models.py | 72 +
partfinder/progress.py | 84 +
partfinder/raxml.py | 348 +
partfinder/raxml_models.py | 90 +
partfinder/reporter.py | 325 +
partfinder/results.py | 98 +
partfinder/scheme.py | 239 +
partfinder/submodels.py | 159 +
partfinder/subset.py | 360 +
partfinder/subset_ops.py | 195 +
partfinder/threadpool.py | 121 +
partfinder/util.py | 223 +
programs/fast_TIGER | Bin 0 -> 237648 bytes
programs/phyml | Bin 0 -> 1073248 bytes
programs/phyml.exe | Bin 0 -> 1476681 bytes
programs/raxml | Bin 0 -> 774196 bytes
programs/raxml.exe | Bin 0 -> 1244406 bytes
programs/raxml_develop | Bin 0 -> 897060 bytes
programs/raxml_rob_SSE3_gcc | Bin 0 -> 1202700 bytes
programs/raxml_rob_SSE3_mac | Bin 0 -> 897060 bytes
programs/raxml_rob_gcc | Bin 0 -> 1169468 bytes
quick_tests.sh | 1 +
tests/PF2/__init__.py | 0
tests/PF2/missing-sites-warning/Als_etal_2004.phy | 5 +
.../PF2/missing-sites-warning/partition_finder.cfg | 13 +
tests/PF2/overlapping-blocks/Als_etal_2004.phy | 5 +
tests/PF2/overlapping-blocks/partition_finder.cfg | 13 +
tests/PF2/test_pf2.py | 36 +
tests/__init__.py | 0
tests/cfg/__init__.py | 0
tests/cfg/test01.cfg | 42 +
tests/cfg/test02.cfg | 42 +
tests/cfg/test03.cfg | 42 +
tests/cfg/test04.cfg | 42 +
tests/cfg/test05.cfg | 42 +
tests/cfg/test06.cfg | 42 +
tests/cfg/test07.cfg | 42 +
tests/cfg/test08.cfg | 42 +
tests/cfg/test09.cfg | 42 +
tests/cfg/test10.cfg | 30 +
tests/cfg/test11.cfg | 24 +
tests/cfg/test12.cfg | 26 +
tests/cfg/test13.cfg | 27 +
tests/cfg/test14.cfg | 25 +
tests/cfg/test15.cfg | 28 +
tests/cfg/test16.cfg | 25 +
tests/cfg/test_configs.py | 52 +
tests/christof/__init__.py | 0
tests/christof/alignment-error/Als_etal_2004.phy | 5 +
.../christof/alignment-error/partition_finder.cfg | 24 +
.../clustering-phyml-dna/partition_finder.cfg | 30 +
tests/christof/clustering-phyml-dna/test.phy | 5 +
.../clustering-raxml-dna/partition_finder.cfg | 30 +
tests/christof/clustering-raxml-dna/test.phy | 5 +
.../christof/greedy-phyml-dna/partition_finder.cfg | 26 +
tests/christof/greedy-phyml-dna/test.phy | 5 +
.../greedy-phyml-protein/Als_etal_2004.phy | 5 +
.../greedy-phyml-protein/partition_finder.cfg | 24 +
.../christof/greedy-raxml-dna/partition_finder.cfg | 30 +
tests/christof/greedy-raxml-dna/test.phy | 5 +
.../greedy-raxml-protein/Als_etal_2004.phy | 5 +
.../greedy-raxml-protein/partition_finder.cfg | 24 +
.../model-greedy-phyml01/Als_etal_2004.phy | 5 +
.../model-greedy-phyml01/partition_finder.cfg | 25 +
.../model-greedy-phyml02/Als_etal_2004.phy | 5 +
.../model-greedy-phyml02/partition_finder.cfg | 24 +
.../model-greedy-phyml03/Als_etal_2004.phy | 5 +
.../model-greedy-phyml03/partition_finder.cfg | 24 +
.../model-greedy-raxml01/Als_etal_2004.phy | 5 +
.../model-greedy-raxml01/partition_finder.cfg | 24 +
.../model-greedy-raxml02/Als_etal_2004.phy | 5 +
.../model-greedy-raxml02/partition_finder.cfg | 25 +
.../model-greedy-raxml03/Als_etal_2004.phy | 5 +
.../model-greedy-raxml03/partition_finder.cfg | 25 +
tests/christof/overlap-error/Als_etal_2004.phy | 5 +
tests/christof/overlap-error/partition_finder.cfg | 24 +
tests/christof/test_christof.py | 86 +
tests/clustering/DNA_hcluster1/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster1/cmdline.txt | 1 +
.../clustering/DNA_hcluster1/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster1/results.bin | 1 +
tests/clustering/DNA_hcluster2/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster2/cmdline.txt | 1 +
.../clustering/DNA_hcluster2/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster2/results.bin | 1 +
tests/clustering/DNA_hcluster3/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster3/cmdline.txt | 1 +
.../clustering/DNA_hcluster3/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster3/results.bin | Bin 0 -> 44 bytes
tests/clustering/DNA_hcluster4/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster4/cmdline.txt | 1 +
.../clustering/DNA_hcluster4/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster4/results.bin | 1 +
tests/clustering/DNA_hcluster5/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster5/cmdline.txt | 1 +
.../clustering/DNA_hcluster5/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster5/results.bin | 1 +
tests/clustering/DNA_hcluster6/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster6/cmdline.txt | 1 +
.../clustering/DNA_hcluster6/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster6/results.bin | 1 +
tests/clustering/DNA_hcluster7/Caterino_2001.phy | 7 +
tests/clustering/DNA_hcluster7/cmdline.txt | 1 +
.../clustering/DNA_hcluster7/partition_finder.cfg | 24 +
tests/clustering/DNA_hcluster7/results.bin | 1 +
tests/clustering/DNA_rcluster1/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster1/cmdline.txt | 1 +
.../clustering/DNA_rcluster1/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster1/results.bin | 1 +
tests/clustering/DNA_rcluster10/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster10/cmdline.txt | 1 +
.../clustering/DNA_rcluster10/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster10/results.bin | 1 +
tests/clustering/DNA_rcluster11/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster11/cmdline.txt | 1 +
.../clustering/DNA_rcluster11/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster11/results.bin | 1 +
tests/clustering/DNA_rcluster12/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster12/cmdline.txt | 1 +
.../clustering/DNA_rcluster12/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster12/results.bin | 1 +
tests/clustering/DNA_rcluster13/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster13/cmdline.txt | 1 +
.../clustering/DNA_rcluster13/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster13/results.bin | 1 +
tests/clustering/DNA_rcluster14/alignment.phy | 66 +
tests/clustering/DNA_rcluster14/cmdline.txt | 1 +
.../clustering/DNA_rcluster14/partition_finder.cfg | 28 +
tests/clustering/DNA_rcluster2/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster2/cmdline.txt | 1 +
.../clustering/DNA_rcluster2/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster2/results.bin | 1 +
tests/clustering/DNA_rcluster3/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster3/cmdline.txt | 1 +
.../clustering/DNA_rcluster3/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster3/results.bin | 1 +
tests/clustering/DNA_rcluster4/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster4/cmdline.txt | 1 +
.../clustering/DNA_rcluster4/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster4/results.bin | 1 +
tests/clustering/DNA_rcluster5/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster5/cmdline.txt | 1 +
.../clustering/DNA_rcluster5/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster5/results.bin | 1 +
tests/clustering/DNA_rcluster6/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster6/cmdline.txt | 1 +
.../clustering/DNA_rcluster6/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster6/results.bin | 1 +
tests/clustering/DNA_rcluster7/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster7/cmdline.txt | 1 +
.../clustering/DNA_rcluster7/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster7/results.bin | 1 +
tests/clustering/DNA_rcluster8/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster8/cmdline.txt | 1 +
.../clustering/DNA_rcluster8/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster8/results.bin | 1 +
tests/clustering/DNA_rcluster9/Caterino_2001.phy | 7 +
tests/clustering/DNA_rcluster9/cmdline.txt | 1 +
.../clustering/DNA_rcluster9/partition_finder.cfg | 24 +
tests/clustering/DNA_rcluster9/results.bin | 1 +
tests/clustering/__init__.py | 0
tests/clustering/prot_hcluster1/cmdline.txt | 1 +
.../clustering/prot_hcluster1/concat_alignment.phy | 11 +
.../clustering/prot_hcluster1/partition_finder.cfg | 25 +
tests/clustering/prot_hcluster1/results.bin | 1 +
tests/clustering/prot_hcluster2/cmdline.txt | 1 +
.../clustering/prot_hcluster2/concat_alignment.phy | 11 +
.../clustering/prot_hcluster2/partition_finder.cfg | 25 +
tests/clustering/prot_hcluster2/results.bin | 1 +
tests/clustering/prot_hcluster3/cmdline.txt | 1 +
.../clustering/prot_hcluster3/concat_alignment.phy | 11 +
.../clustering/prot_hcluster3/partition_finder.cfg | 22 +
tests/clustering/prot_hcluster3/results.bin | 1 +
tests/clustering/prot_rcluster1/cmdline.txt | 1 +
.../clustering/prot_rcluster1/concat_alignment.phy | 11 +
.../clustering/prot_rcluster1/partition_finder.cfg | 25 +
tests/clustering/prot_rcluster1/results.bin | 1 +
tests/clustering/prot_rcluster2/cmdline.txt | 1 +
.../clustering/prot_rcluster2/concat_alignment.phy | 11 +
.../clustering/prot_rcluster2/partition_finder.cfg | 25 +
tests/clustering/prot_rcluster2/results.bin | 1 +
tests/clustering/prot_rcluster3/cmdline.txt | 1 +
.../clustering/prot_rcluster3/concat_alignment.phy | 11 +
.../clustering/prot_rcluster3/partition_finder.cfg | 25 +
tests/clustering/prot_rcluster3/results.bin | 1 +
tests/clustering/prot_rcluster4/cmdline.txt | 1 +
.../clustering/prot_rcluster4/concat_alignment.phy | 11 +
.../clustering/prot_rcluster4/partition_finder.cfg | 25 +
tests/clustering/prot_rcluster4/results.bin | 1 +
tests/clustering/prot_rcluster5/cmdline.txt | 1 +
.../clustering/prot_rcluster5/concat_alignment.phy | 11 +
.../clustering/prot_rcluster5/partition_finder.cfg | 25 +
tests/clustering/prot_rcluster5/results.bin | 1 +
tests/clustering/test_clustering.py | 86 +
tests/clustering/tests.txt | 36 +
tests/full_analysis/DNA1/Caterino_2001.phy | 7 +
tests/full_analysis/DNA1/partition_finder.cfg | 28 +
tests/full_analysis/DNA1/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA2/Caterino_2001.phy | 7 +
tests/full_analysis/DNA2/partition_finder.cfg | 28 +
tests/full_analysis/DNA2/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA3-analysis.zip | Bin 0 -> 246602 bytes
tests/full_analysis/DNA3/Caterino_2001.phy | 7 +
tests/full_analysis/DNA3/partition_finder.cfg | 28 +
tests/full_analysis/DNA3/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA4/Caterino_2001.phy | 7 +
tests/full_analysis/DNA4/partition_finder.cfg | 28 +
tests/full_analysis/DNA4/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA5/Caterino_2001.phy | 7 +
tests/full_analysis/DNA5/partition_finder.cfg | 28 +
tests/full_analysis/DNA5/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA6/Caterino_2001.phy | 7 +
tests/full_analysis/DNA6/partition_finder.cfg | 28 +
tests/full_analysis/DNA6/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA7/Caterino_2001.phy | 7 +
tests/full_analysis/DNA7/partition_finder.cfg | 28 +
tests/full_analysis/DNA7/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/DNA8/Caterino_2001.phy | 7 +
tests/full_analysis/DNA8/partition_finder.cfg | 28 +
tests/full_analysis/DNA8/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/__init__.py | 0
tests/full_analysis/kmeans1/alignment.phy | 1 +
tests/full_analysis/kmeans1/partition_finder.cfg | 17 +
tests/full_analysis/kmeans_fast/alignment.phy | 1 +
.../full_analysis/kmeans_fast/partition_finder.cfg | 17 +
tests/full_analysis/kmeans_fast/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/prot1/concat_alignment.phy | 11 +
tests/full_analysis/prot1/partition_finder.cfg | 27 +
tests/full_analysis/prot1/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/prot2/concat_alignment.phy | 11 +
tests/full_analysis/prot2/partition_finder.cfg | 27 +
tests/full_analysis/prot2/results.bin | 1 +
tests/full_analysis/prot3/concat_alignment.phy | 11 +
tests/full_analysis/prot3/partition_finder.cfg | 27 +
tests/full_analysis/prot3/results.bin | 1 +
tests/full_analysis/prot4/concat_alignment.phy | 11 +
tests/full_analysis/prot4/partition_finder.cfg | 27 +
tests/full_analysis/prot4/results.bin | 1 +
tests/full_analysis/prot5/concat_alignment.phy | 11 +
tests/full_analysis/prot5/partition_finder.cfg | 27 +
tests/full_analysis/prot5/results.bin | 1 +
tests/full_analysis/prot6/concat_alignment.phy | 11 +
tests/full_analysis/prot6/partition_finder.cfg | 27 +
tests/full_analysis/prot6/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/prot7/concat_alignment.phy | 11 +
tests/full_analysis/prot7/partition_finder.cfg | 27 +
tests/full_analysis/prot7/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/prot8/concat_alignment.phy | 11 +
tests/full_analysis/prot8/partition_finder.cfg | 27 +
tests/full_analysis/prot8/results.bin | Bin 0 -> 131 bytes
tests/full_analysis/rerun01/Caterino_2001.phy | 7 +
tests/full_analysis/rerun01/partition_finder.cfg | 28 +
tests/full_analysis/rerun02/Caterino_2001.phy | 7 +
tests/full_analysis/rerun02/partition_finder.cfg | 28 +
tests/full_analysis/rerun03/Caterino_2001.phy | 7 +
tests/full_analysis/rerun03/partition_finder.cfg | 28 +
tests/full_analysis/rerun04/Caterino_2001.phy | 7 +
tests/full_analysis/rerun04/partition_finder.cfg | 28 +
tests/full_analysis/rerun05/Caterino_2001.phy | 7 +
tests/full_analysis/rerun05/partition_finder.cfg | 28 +
tests/full_analysis/rerun06/Caterino_2001.phy | 7 +
tests/full_analysis/rerun06/partition_finder.cfg | 28 +
tests/full_analysis/rerun07/Caterino_2001.phy | 7 +
tests/full_analysis/rerun07/partition_finder.cfg | 28 +
tests/full_analysis/rerun08/Caterino_2001.phy | 7 +
tests/full_analysis/rerun08/partition_finder.cfg | 28 +
tests/full_analysis/rerun09/Caterino_2001.phy | 7 +
tests/full_analysis/rerun09/partition_finder.cfg | 28 +
tests/full_analysis/rerun10/Caterino_2001.phy | 7 +
tests/full_analysis/rerun10/partition_finder.cfg | 28 +
tests/full_analysis/rerun11/Caterino_2001.phy | 7 +
tests/full_analysis/rerun11/partition_finder.cfg | 28 +
tests/full_analysis/rerun12/Caterino_2001.phy | 7 +
tests/full_analysis/rerun12/partition_finder.cfg | 28 +
tests/full_analysis/rerun13/Caterino_2001.phy | 7 +
tests/full_analysis/rerun13/partition_finder.cfg | 28 +
tests/full_analysis/rerun14/Caterino_2001.phy | 7 +
tests/full_analysis/rerun14/partition_finder.cfg | 28 +
tests/full_analysis/rerun15/Caterino_2001.phy | 7 +
tests/full_analysis/rerun15/partition_finder.cfg | 28 +
tests/full_analysis/rerun16/Caterino_2001.phy | 7 +
tests/full_analysis/rerun16/partition_finder.cfg | 28 +
tests/full_analysis/rerun17/Caterino_2001.phy | 7 +
tests/full_analysis/rerun17/partition_finder.cfg | 25 +
tests/full_analysis/rerun18/Caterino_2001.phy | 7 +
tests/full_analysis/rerun18/partition_finder.cfg | 23 +
tests/full_analysis/rerun19/Caterino_2001_ooh.phy | 7 +
tests/full_analysis/rerun19/partition_finder.cfg | 28 +
tests/full_analysis/rerun20/Caterino_2001.phy | 7 +
tests/full_analysis/rerun20/partition_finder.cfg | 28 +
tests/full_analysis/rerun21/Caterino_2001.phy | 7 +
tests/full_analysis/rerun21/partition_finder.cfg | 28 +
tests/full_analysis/test_full.py | 64 +
tests/full_analysis/tests.txt | 79 +
tests/kmeans/Grande_2013/README.yaml | 23 +
tests/kmeans/Grande_2013/alignment.phy | 66 +
tests/kmeans/Grande_2013/partition_finder.cfg | 19 +
tests/kmeans/__init__.py | 0
tests/kmeans/fabrications1/README.yaml | 23 +
tests/kmeans/fabrications1/alignment.phy | 6 +
tests/kmeans/fabrications1/partition_finder.cfg | 17 +
tests/kmeans/fabrications2/README.yaml | 23 +
tests/kmeans/fabrications2/alignment.phy | 7 +
tests/kmeans/fabrications2/partition_finder.cfg | 22 +
tests/kmeans/test_kmeans.py | 10 +
tests/misc/Caterino_2001.phy | 7 +
tests/misc/interleave.phy | 133 +
tests/misc/raxml_aminoacid.output | 301 +
tests/misc/raxml_aminoacid_LG4M+G.output | 942 +
tests/misc/raxml_nucleotide.output | 66 +
tests/nuc_single_site/partition_finder.cfg | 46 +
tests/nuc_single_site/single_site.phy | 33 +
tests/paul/RAxML_perSiteLLs.testing | 2 +
tests/paul/__init__.py | 0
tests/paul/fabricated/fabricated.phy | 11 +
tests/paul/fabricated/partition_finder.cfg | 34 +
tests/paul/free_rates_4_cat.phy_phyml_lk.txt | 17 +
tests/paul/gamma_8_cat.phy_phyml_lk.txt | 17 +
tests/paul/simulated_TRUE.phy_phyml_lk.txt | 14 +
tests/quick_analysis/__init__.py | 0
tests/quick_analysis/all/partition_finder.cfg | 32 +
tests/quick_analysis/all/random.phy | 7 +
tests/quick_analysis/aln_RY/partition_finder.cfg | 36 +
tests/quick_analysis/aln_RY/random.phy | 132 +
.../aln_interleaved/partition_finder.cfg | 36 +
tests/quick_analysis/aln_interleaved/random.phy | 132 +
tests/quick_analysis/greedy/partition_finder.cfg | 32 +
tests/quick_analysis/greedy/random.phy | 7 +
.../maclinebreaks/partition_finder.cfg | 1 +
tests/quick_analysis/maclinebreaks/random.phy | 1 +
tests/quick_analysis/test_quick.py | 27 +
tests/quick_analysis/user/partition_finder.cfg | 36 +
tests/quick_analysis/user/random.phy | 7 +
.../quick_analysis/user_tree/partition_finder.cfg | 33 +
tests/quick_analysis/user_tree/random.phy | 7 +
tests/quick_analysis/user_tree/tree.phy | 1 +
.../windowslinebreaks/partition_finder.cfg | 36 +
tests/quick_analysis/windowslinebreaks/random.phy | 7 +
tests/test_alignment.py | 109 +
tests/test_options.py | 23 +
tests/test_parser.py | 39 +
tests/test_raxml.py | 46 +
tests/test_submodels.py | 27 +
tests/test_subset.py | 41 +
tests/test_tiger.py | 97 +
timings/array_lookups.py | 179 +
timings/numpy_vs_set.py | 42 +
402 files changed, 34828 insertions(+)
diff --git a/.gitignore b/.gitignore
new file mode 100644
index 0000000..3e8b332
--- /dev/null
+++ b/.gitignore
@@ -0,0 +1,56 @@
+tags
+partition_finder.tmproj
+*.pyc
+.idea
+partfinder.log
+example/analysis
+tests/testing.log
+log.txt
+.lock*
+.waf*
+programs/phyml_source/build/
+.noseids
+example/results.bin
+.DS_Store
+.ropeproject
+analysis
+.cache
+*.so
+*.o
+build
+
+examples/nucleotide/best_scheme_GTR+G.txt
+
+examples/nucleotide/best_scheme_GTR+I+G.txt
+
+examples/nucleotide/best_scheme_JC.txt
+
+examples/nucleotide/best_scheme_all_models.txt
+
+examples/aminoacid/best_scheme_greedy.txt
+
+examples/aminoacid/Als_etal_2004.phy_phyml_lk.txt
+
+examples/aminoacid/Als_etal_2004.phy_phyml_stats.txt
+
+examples/aminoacid/Als_etal_2004.phy_phyml_tree.txt
+
+examples/aminoacid/best_scheme_kmeans_site_likelihoods.txt
+
+examples/aminoacid/best_scheme_kmeans_site_lnl_genes.txt
+
+examples/aminoacid/filtered_source.phy_phyml_tree.txt
+
+examples/nucleotide/best_scheme_greedy_codon_genes.txt
+
+examples/nucleotide/best_scheme_greedy_genes.txt
+
+examples/aminoacid/best_scheme_raxml_site_lnl_genes.txt
+
+examples/nucleotide/test.phy.GENE.8
+examples/nucleotide/test.phy.reduced
+examples/nucleotide/RAxML_info.partitions
+examples/nucleotide/best_scheme_all_models_kmeans_wss.txt
+examples/nucleotide/raxml_def_all_models_wss.txt
+docs/.Rhistory
+docs/.Rapp.history
diff --git a/.gitmodules b/.gitmodules
new file mode 100644
index 0000000..47147c1
--- /dev/null
+++ b/.gitmodules
@@ -0,0 +1,8 @@
+[submodule "submodules/raxml"]
+ path = submodules/raxml
+ url = https://brettc@github.com/brettc/standard-RAxML.git
+ branch = partfinder
+[submodule "submodules/phyml"]
+ path = submodules/phyml
+ url = https://brettc@github.com/brettc/phyml.git
+ branch = partfinder
diff --git a/PartitionFinder.py b/PartitionFinder.py
new file mode 100644
index 0000000..6ef5fbc
--- /dev/null
+++ b/PartitionFinder.py
@@ -0,0 +1,23 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import sys
+from partfinder import main
+
+if __name__ == "__main__":
+ # Well behaved unix programs exits with 0 on success...
+ sys.exit(main.main("PartitionFinder", "DNA"))
diff --git a/PartitionFinderProtein.py b/PartitionFinderProtein.py
new file mode 100644
index 0000000..2c5517d
--- /dev/null
+++ b/PartitionFinderProtein.py
@@ -0,0 +1,23 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import sys
+from partfinder import main
+
+if __name__ == "__main__":
+ # Well behaved unix programs exits with 0 on success...
+ sys.exit(main.main("PartitionFinderProtein", "protein"))
diff --git a/README.md b/README.md
new file mode 100644
index 0000000..18d401f
--- /dev/null
+++ b/README.md
@@ -0,0 +1,38 @@
+# PartitionFinder
+
+PartitionFinder and PartitionFinderProtein are Python programs for simultaneously
+choosing partitioning schemes and models of molecular evolution for sequence data.
+You can use them before running a phylogenetic analysis, in order
+to decide how to divide up your sequence data into separate blocks before
+analysis, and to simultaneously perform model selection on each of those
+blocks.
+
+# Operating System
+
+Mac and Windows are supported.
+All of the code was written with Linux in mind too, so if you are interested
+in porting it to Linux, please get in touch (or just try it out!).
+
+# Manual
+
+is in the /docs folder.
+
+# Quick Start
+
+* Make sure you have the Anaconda Python distribution version 2.3.0 or higher, and make sure it's the one that ships with Python 2, and that the version number of Python is at least 2.7.10 (you do not want the anaconda distribution that gives you Python 3.x). http://continuum.io/downloads.
+
+* For PartitionFinderProtein just substitute 'PartitionFinderProtein' for 'PartitionFinder' below
+
+1. Open Terminal (on a Mac) or Command Prompt (on Windows) and cd to the directory with PartitionFinder in it
+2. Run PartitionFinder by typing at the command prompt:
+
+ python PartitionFinder.py examples/nucleotide
+
+This will run the included example analysis for PartitionFinder. More generally, the command line for PartitionFinder looks like this:
+
+ python <PartitionFinder.py> <foldername>
+
+where <PartitionFinder.py> is the full file-path to the PartitionFinder.py file
+and <foldername> is the full filepath to a folder with a phylip alignemnt and associated .cfg file.
+
+For more details, read the manual.
diff --git a/all_tests.sh b/all_tests.sh
new file mode 100644
index 0000000..fea3d75
--- /dev/null
+++ b/all_tests.sh
@@ -0,0 +1 @@
+py.test -v
diff --git a/build_ext.py b/build_ext.py
new file mode 100644
index 0000000..9fa7555
--- /dev/null
+++ b/build_ext.py
@@ -0,0 +1,33 @@
+from distutils.core import setup
+from distutils.extension import Extension
+from Cython.Build import cythonize
+import numpy
+import sys
+
+# This file is only used for compiling tigger, so let's just make it do this
+# by default. This only works for Mac right now.
+sys.argv = ['build_ext.py', 'build_ext', '--inplace']
+
+# CFLAGS
+# -Wno-unused-function
+extensions = [
+ Extension(
+ "partfinder/_tiger",
+ ["partfinder/_tiger.pyx"],
+ extra_compile_args=[
+ '-Wno-unused-function',
+ '-stdlib=libc++',
+ '-std=c++11',
+ '-mmacosx-version-min=10.8',
+ ],
+ language='c++',
+ )
+]
+setup(
+ name='partfinder',
+ ext_modules=cythonize(
+ extensions,
+ aliases={'NUMPY_PATH': numpy.get_include()},
+ nthreads=4,
+ ),
+)
diff --git a/build_programs.sh b/build_programs.sh
new file mode 100644
index 0000000..9327b79
--- /dev/null
+++ b/build_programs.sh
@@ -0,0 +1,30 @@
+# Get the submodules (raxml and phyml)
+git submodule init
+git submodule update
+
+# Building Phyml ----------------------------------
+# This is modified from the confphy...
+# It assumes that you've done:
+# brew install automake autoconf libtool
+cd submodules/phyml
+aclocal
+autoheader
+autoconf -f
+# Note: brew renames this...
+glibtoolize
+automake -f --add-missing
+./configure
+make clean
+make
+
+cd ../..
+mv -f ./submodules/phyml/src/phyml ./programs
+
+
+# Building Raxml ----------------------------------
+# We use the SSE as it is the most reliable
+cd submodules/raxml
+make -f Makefile.SSE3.gcc
+
+cd ../..
+mv -f ./submodules/raxml/raxmlHPC-SSE3 ./programs/raxml
diff --git a/clean_tests.sh b/clean_tests.sh
new file mode 100644
index 0000000..6b2c3e4
--- /dev/null
+++ b/clean_tests.sh
@@ -0,0 +1,2 @@
+find . -name analysis -and -d | xargs rm -rf
+find . -name log.txt | xargs rm
diff --git a/docs/Figure1.pptx b/docs/Figure1.pptx
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diff --git a/docs/README.md b/docs/README.md
new file mode 100644
index 0000000..1ef4450
--- /dev/null
+++ b/docs/README.md
@@ -0,0 +1,119 @@
+#Using PartitionFinder for enormous datasets
+
+##Install Anaconda
+This just makes sure that you have the latest Python libraries that PartitionFinder needs.
+
+1. Go to this address and follow the instructions for your system:
+http://docs.continuum.io/anaconda/install.html
+
+2. Check that it worked by typing this at the command prompt:
+ conda
+
+It should print out a lot of help stuff for anaconda.
+
+##Install PartitionFinder
+We need the development version of PartitionFinder (it will be PF2, but it's not quite ready for general release, yet):
+
+1. Go to here to get the zip file:
+https://github.com/brettc/partitionfinder/archive/develop.zip
+
+2. Unzip develop.zip which will create a folder called partitionfinder-develop
+
+3. If you are using Linux, you will need to download and compile your own version of RAxML. To do that:
+
+ 3.1 Download the PF version of RAxML from here:
+ https://github.com/brettc/standard-RAxML/archive/master.zip
+
+ 3.2 Compile using the Makefile.SSE3.gcc, or the Makefile.AVX.gcc version, depending on your chip architecture, following the instructions here (do not use the PTHREADs or MPI versions, and do not use the RAxML from Alexis Statmatakis' github account):
+ https://github.com/brettc/standard-RAxML
+
+ 3.3 Rename the compiled executable "raxml"
+
+ 3.4 In the 'partitionfinder-develop/programs' folder, delete 'raxml'
+ copy-paste your newly compiled 'raxml' into partitionfinder-develop/programs folder
+
+
+##Run PartitionFinder
+Setting up the .cfg file still works exactly as described in the manaul (in the /docs folder). There are just a few additional options you should know about, that are not yet described in the manual.
+
+
+--rcluster-max
+
+defines the number of partitioning scheme that PF will explore at each step of the analysis. More is better, and the default is 1000. As a rough rule of thumb, I suggest using 2x the number of data blocks in your .cfg file. If your run is too slow, make --rcluster-max smaller. We have to be pragmatic, after all. But if your run finishes quickly, try running it again after doubling --rcluster max.
+
+-q
+
+this stops PF from writing unnecessary files. And helps you to stay friends with the folks that manage the clusters you might use.
+
+By default PF will use ALL of your CPUs. To control the number of cpus, use -p:
+
+e.g. "-p 10" will use 10 cpus (or less than 10 if you have less than 10).
+
+##An example
+Here's a worked example of analysing a massive dataset with PartitionFinder.
+
+###Example partition_finder.cfg file
+Let's imagine we're running a very large amino acid dataset, with 1000's of species, and 1000's of data blocks. Our .cfg file might look something like this:
+
+ alignment = alignment.phy;
+
+ branchlengths = linked;
+
+ models = LG+G, LG+G+F;
+
+ model_selection = AICc;
+
+ [data_blocks]
+
+ Gene1 = 1 - 609 ;
+ Gene2 = 610 - 1409;
+ Gene3 = 1410 - 1560;
+ ... [LOTS MORE DATA BLOCKS HERE]
+
+ [schemes]
+ search = rcluster;
+
+Let's go through each line in turn.
+
+'alignment' just points the alignment file. Name it whatever your alignment is called.
+
+'branchlengths' should be set to linked. You can try 'unlinked' if you like, but this invovles estimating a LOT more paratmeters and is almost never preferred over linked branch lengths. In almost all cases, it's fine to just assume that 'linked' is the best option.
+
+'models' defines the models we want to use. See the manual for a list of what's possible (we have to stick to raxml models here). I've defined a very small model list here, because analysing very big datasets can take a long time. So it's worth thinking carefully about how to reduce the number of models you're analysing. In general, twice the number of models will take twice as long to analyse. Also be aware that, if you're planning to analyse your data in RAxML after you do the partitio [...]
+
+'model_selection': just choose your favourite metric from AICc and BIC. The AIC is not recommended, becuase it's asymptotically the same as the AICc as dat blocks get very big, but the AICc is more sensible for smaller data blocks.
+
+'[data blocks]': look at the manual to see how to define these.
+
+'search': stick to 'rcluster' for giant datasets. Just use --rcluster-max at the command line to control the algorithm (see above).
+
+###Example command line
+I'm assuming you've read the manual before you read this. I'm not going to explain anything that's already in the manual.
+
+Here's an example of running PF the simplest way we can for our .cfg file above (assuming there are no errors in your .cfg file or alignment):
+
+ python ~/blah/PartitionFinderProtein.py ~/blah/analysis --raxml
+
+We need the "--raxml" to tell PF to use raxml - the rcluster algorithm only works with raxml. And in general if you're working with massive datasets, you'll be using raxml too.
+
+It's probably a good idea with massive datasets to avoid any unneccesary file writing by using the -q option:
+
+ python ~/blah/PartitionFinderProtein.py ~/blah/analysis --raxml -q
+
+If we want to control the relaxed clustering algorithm, we have a few options. We can make it more thorough than the default by increasing the number of schemes it looks at:
+
+ python ~/blah/PartitionFinderProtein.py ~/blah/analysis --raxml -q --rcluster-max 5000
+
+If you want to control the number of processors, use -p:
+
+ python ~/blah/PartitionFinderProtein.py ~/blah/analysis --raxml -q --rcluster-max 5000 -p 20
+
+And if you want to control the way that similarity is defined among subsets, you can use the "--weights" option (see the manual for how this works). For example, we could assign equal weight to rates, amino acid frequencies, and the gamma parameter, but ignore model parameters (sensible for an amino acid dataset because they are not estimated from the data):
+
+ python ~/blah/PartitionFinderProtein.py ~/blah/analysis --raxml -q --rcluster-max 5000 -p 20 --weights "1, 1, 0, 1"
+
+
+
+
+
+
diff --git a/docs/citationsplot.pdf b/docs/citationsplot.pdf
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index 0000000..3fdd91b
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diff --git a/docs/citationsplot2.pdf b/docs/citationsplot2.pdf
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diff --git a/docs/downloadplot.pdf b/docs/downloadplot.pdf
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index 0000000..3a21c48
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diff --git a/docs/downloadplot.r b/docs/downloadplot.r
new file mode 100644
index 0000000..a24dfb3
--- /dev/null
+++ b/docs/downloadplot.r
@@ -0,0 +1,64 @@
+library(ggplot2)
+library(reshape)
+library(zoo)
+
+dat <- read.csv("~/Documents/github/partitionfinder/docs/downloadstats.csv")
+dat$date <- as.yearmon(dat$date)
+dat <- aggregate(. ~ date, data=dat, FUN=sum, na.action=na.pass)
+dat <- dat[order(as.Date(dat$date)),]
+
+dat$Mac <- cumsum(dat$Mac)
+dat$Windows <- cumsum(dat$Windows)
+
+
+# Download plot
+m <- dat[,c(1,2)]
+m$OS <- "Mac"
+names(m) <- c('date', 'downloads', 'OS')
+w <- dat[,c(1,3)]
+w$OS <- "Windows"
+names(w) <- c('date', 'downloads', 'OS')
+
+dl <- rbind(m, w)
+dl$date <- as.Date(dl$date, format = "%d/%m/%Y")
+
+quartz(width=10, height=5)
+p <- ggplot(dl, aes(date, downloads))
+p + geom_area(aes(colour = OS, fill= OS), position = 'stack')
+dev.copy2pdf(file="~/Documents/github/partitionfinder/docs/downloadplot.pdf")
+dev.off()
+
+
+# Citation plot
+c <- dat[,c(1,5)]
+c$date <- as.Date(c$date, format = "%d/%m/%Y")
+c <- c[complete.cases(c),]
+
+quartz(width=10, height=5)
+p <- ggplot(c, aes(date, citations.googlescholar))
+p + geom_point() + geom_smooth(stat="identity")
+dev.copy2pdf(file="~/Documents/github/partitionfinder/docs/citationsplot.pdf")
+dev.off()
+
+
+# Conversion rate plot (how many downloads per citation)
+d <- c[c(2:nrow(c)),]
+d$downloads <- m$downloads[19:length(m$downloads)] + m$downloads[19:length(m$downloads)]
+d$downloads.per.cite <- d$downloads / d$citations.googlescholar
+
+e <- d[,c(1,2)]
+e$type <- "citations"
+f <- d[,c(1,4)]
+f$type <- "downloads.per.citation"
+
+names(e) <- names(f) <- c("date", "value", "type")
+g <- rbind(e, f)
+
+quartz(width=10, height=5)
+p <- ggplot(f, aes(date, downloads.per.cite, colour = type))
+p + geom_point() + geom_smooth(stat="identity")
+dev.copy2pdf(file="~/Documents/github/partitionfinder/docs/citationsplot2.pdf")
+dev.off()
+
+
+
diff --git a/docs/downloadstats.csv b/docs/downloadstats.csv
new file mode 100644
index 0000000..209e9ef
--- /dev/null
+++ b/docs/downloadstats.csv
@@ -0,0 +1 @@
+date,Mac,Windows,version,citations.googlescholar,citations.added.per.month
2012-01,30,0,0.9,10,
2012-02,66,0,0.9,NA,
2012-03,28,0,0.9,NA,
2012-03,44,0,0.9.2,NA,
2012-04,39,0,0.9.2,NA,
2012-05,70,48,1.0.0,NA,
2012-06,35,58,1.0.0,NA,
2012-07,41,54,1.0.0,NA,
2012-08,107,190,1.0.1,NA,
2012-09,68,95,1.0.1,NA,
2012-10,62,65,1.0.1,NA,
2012-11,50,76,1.0.1,NA,
2012-12,62,126,1.0.1,NA,
2013-01,88,1075,1.0.1,NA,
2013-02,72,252,1.0.1,NA,
2013-03,108,152,1.0.1,NA,
2013-04,100,127,1.0.1,NA,
2013-05,59,68,1.0.1,NA,
2013-05,51,50,1.1.0,NA,
2013-06,50,58,1.1.0,NA,
2013-06,101,86,1.1.1,49,
2013-07,96,114,1.1.1,56,7
2013-08,94,119,1.1.1,63,7
2013-09,188,104,1.1.1,77,14
2013-10,123,108,1.1.1,92,15
2013-11,96,167,1.1.1,102,10
2013-12,69,100,1.1.1,117,13
2014-1,61,103,1.1.1,131,14
2014-2,138,150,1.1.1,141,10
2014-3,106,332,1.1.1,161,20
2014-4,121,266,1.1.1,182,21
2014-5,177,841,1.1.1,202,20
2014-6,165,596,1.1.1,231,29
2014-7,379,590,1.1.1,251,20
2014-8,379,499,1.1.1,279,28
2014-9,506,526,1.1.1,301,22
2014-10,486,617,1.1.1,331,30
2014-11,126,702,1.1.1,363,33
2014-12,80,658,1.1.1,402,39
2015-1,112,626,1.1.1,433,31
2015-2,133,467,1.1.1,458,25
2015-3,212,510,1.1.1,494,36
2015-4,147,424,1.1.1,532,38
2015-5,124,585,1.1.1,572,40
2015-6,111,648,1.1.1,623,51
2015-7,120,716,1.1.1,648,25
2015-8,120,743,1.1.1,698,50
\ No newline at end of file
diff --git a/docs/evoldir_annoucement_1.txt b/docs/evoldir_annoucement_1.txt
new file mode 100644
index 0000000..ae64386
--- /dev/null
+++ b/docs/evoldir_annoucement_1.txt
@@ -0,0 +1,29 @@
+Dear all,
+
+We're pleased to announce the release of PartitionFinder v1.0.1, a program for the combined selection of partitioning schemes and models of molecular evolution for phylogenetic analyses.
+
+PartitionFinder automatically and objectively finds best-fit partitioning schemes for DNA and protein alignments, and also does all of the model selection into the bargain. It means you no longer have to spend a long time evaluating partitioning schemes and running model selection programs before you can run your phylogenetic analyses. Detailed instructions on installing and using PartitionFinder are provided in the manual. PartitionFinder is free and open source. It works on Windows, Ma [...]
+
+You can download PartitionFinder from here:
+
+www.robertlanfear.com/partitionfinder
+
+The website also has links to the manual, FAQs, a tutorial, and a google group for questions.
+
+A paper describing the program came out earlier this year in MBE:
+http://mbe.oxfordjournals.org/content/29/6/1695
+
+PartitionFinder can be used for the following:
+
+ * Find best-fit partitioning schemes for DNA and protein datasets, given a set of starting partitions
+ * Calculate the AIC, AICc and BIC of any given partitioning scheme for any given dataset
+ * Calculate best fit models of molecular evolution for partitioned or unpartitioned datasets
+ * Compare all the usual models of molecular evolution for DNA and protein alignments
+
+We are actively working on the program, so please do get in touch if you have questions, suggestions, or comments.
+
+Yours
+
+Rob Lanfear
+
+rob.lanfear at anu.edu.au
\ No newline at end of file
diff --git a/docs/evoldir_annoucement_2.txt b/docs/evoldir_annoucement_2.txt
new file mode 100644
index 0000000..3af8287
--- /dev/null
+++ b/docs/evoldir_annoucement_2.txt
@@ -0,0 +1,41 @@
+Dear all,
+
+We're pleased to announce the release of PartitionFinder v1.1.1.
+This version contains a number of major improvements over previous
+versions, including the ability to rapidly analyse genomic datasets.
+
+PartitionFinder is a program that allows for the combined selection
+of partitioning schemes and models of molecular evolution for DNA
+and amino acid datasets. It works on Windows, Mac, and Linux.
+
+It is available here:
+
+www.robertlanfear.com/partitionfinder
+
+Version 1.1.1 includes a number of improvements:
+
+ * Support for very large datasets (1000s of genes, 1000s of taxa)
+ * Faster algorithms
+ * Support for partitioning scheme searches using RAxML
+ * Improved memory efficiency
+ * Output of the best partitioning scheme in RAxML format
+ * A number of bug fixes and other minor improvements
+
+A full description of all the methods can be found in the manual, along
+with some hints on the best method to use for datasets of different sizes.
+The methods are more fully described and compared in an in prep paper.
+
+Please get in touch if you have questions, suggestions, or comments.
+
+Yours,
+
+Rob Lanfear & Brett Calcott
+
+--
+Rob Lanfear
+Research Fellow,
+Ecology, Evolution, and Genetics,
+Research School of Biology,
+Australian National University
+
+www.robertlanfear.com
diff --git a/docs/googlegroup_analysis.r b/docs/googlegroup_analysis.r
new file mode 100644
index 0000000..83abb1f
--- /dev/null
+++ b/docs/googlegroup_analysis.r
@@ -0,0 +1,10 @@
+d <- read.csv("~/Documents/Projects_Current/partitionfinder/docs/googlegroup_stats.csv")
+
+format = "%a, %d %b %Y %H:%M:%S"
+
+d$Sent <- strptime(d$Sent, format=format)
+d$Replied <- strptime(d$Replied, format=format)
+
+d$ResponseTime <- d$Replied - d$Sent
+
+median(d$ResponseTime)
diff --git a/docs/googlegroup_stats.csv b/docs/googlegroup_stats.csv
new file mode 100644
index 0000000..9c2dd8f
--- /dev/null
+++ b/docs/googlegroup_stats.csv
@@ -0,0 +1 @@
+MessageID,Sent,Replied
2,"Tue, 19 Jul 2011 01:39:48","Tue, 19 Jul 2011 01:50:49"
3,"Wed, 03 Aug 2011 06:03:58","Wed, 03 Aug 2011 06:06:17"
4,"Thu, 11 Aug 2011 18:17:15","Thu, 11 Aug 2011 18:38:33"
5,"Tue, 09 Aug 2011 15:35:50","Tue, 09 Aug 2011 15:53:59"
6,"Tue, 27 Dec 2011 14:17:37","Tue, 27 Dec 2011 14:27:29"
7,"Sat, 18 Feb 2012 13:45:47","Sat, 18 Feb 2012 13:51:26"
8,"Fri, 02 Mar 2012 21:45:40","Sun, 04 Mar 2012 13:41:47"
9,"Wed, 07 Mar 2012 02:39:05","Wed, 07 Mar 2012 02:43:18"
10,"Sun, 11 Mar 2012 06:13:07","Sun, 11 Mar 2012 06:17:51"
11,"Tue, 15 May 2012 21:09:45","Tue, 15 May 2012 21:49:57"
12,"Wed, 06 Jun 2012 01:54:58","Wed, 06 Jun 2012 03:45:59"
13,"Mon, 27 Aug 2012 06:04:50","Tue, 28 Aug 2012 11:53:29"
14,"Wed, 29 Aug 2012 04:31:26","Wed, 29 Aug 2012 04:42:33"
15,"Fri, 14 Sep 2012 07:32:06","Fri, 14 Sep 2012 07:51:04"
16,"Mon, 01 Oct 2012 06:56:15","Mon, 01 Oct 2012 10:05:06"
17,"Fri, 05 Oct 2012 13:09:59","Fri, 5 Oct 2012 13:24:49"
18,"Tue, 9 Oct 2012 11:51:45","Tue, 09 Oct 2012 13:09:53"
19,"Tue, 9 Oct 2012 11:34:57","Tue, 09 Oct 2012 13:08:10"
20,"Mon, 22 Oct 2012 10:40:43","Mon, 22 Oct 2012 15:09:29"
21,"Mon, 17 Dec 2012 13:18:59","Mon, 17 Dec 2012 13:20:45"
22,"Mon, 31 Dec 2012 22:35:32","Mon, 31 Dec 2012 23:50:20"
23,"Thu, 10 Jan 2013 10:35:21","Thu, 10 Jan 2013 11:01:21"
24,"Fri, 01 Mar 2013 11:57:01","Fri, 01 Mar 2013 12:01:46"
25,"Sat, 01 Dec 2012 16:22:00","Sat, 01 Dec 2012 16:26:13"
26,"Fri, 15 Mar 2013 14:41:45","Fri, 15 Mar 2013 14:51:35"
27,"Tue, 19 Mar 2013 14:10:28","Tue, 19 Mar 2013 14:23:31"
28,"Thu, 28 Feb 2013 14:10:16","Fri, 01 Mar 2013 12:05:32"
29,"Tue, 02 Apr 2013 14:30:33","Tue, 2 Apr 2013 14:34:06"
30,"Fri, 12 Apr 2013 17:23:54","Fri, 12 Apr 2013 17:34:51"
31,"Wed, 17 Apr 2013 19:27:26","Wed, 17 Apr 2013 19:30:11"
32,"Mon, 22 Apr 2013 15:05:02","Mon, 22 Apr 2013 15:11:39"
33,"Sat, 27 Apr 2013 09:17:58","Sat, 27 Apr 2013 14:38:12"
34,"Fri, 31 May 2013 06:42:14","Fri, 31 May 2013 06:44:22"
35,"Fri, 07 Jun 2013 12:01:45","Fri, 07 Jun 2013 12:09:21"
36,"Fri, 14 Jun 2013 04:49:38","Fri, 14 Jun 2013 05:07:14"
\ No newline at end of file
diff --git a/docs/tiger_compilation.txt b/docs/tiger_compilation.txt
new file mode 100644
index 0000000..55a7a90
--- /dev/null
+++ b/docs/tiger_compilation.txt
@@ -0,0 +1,51 @@
+Instructions for compiling fast_TIGER and the cython version of tiger.
+
+fast_TIGER:
+
+Pre-requisites:
+On a Mac, you should have a compiler installed (mac uses llvm instead of gcc now, it seems to work just fine). If you are working with OSX Yosemite, you can do this by downloading the most recent version of XCode from the Mac App store. Once XCode is installed, open it and install any updates that it requires.
+
+Next, open a terminal window and enter the command, 'xcode-select --install'. This will allow you to install the command line tools for XCode. After this is done, you should exit your terminal session.
+
+fast_TIGER install:
+
+- Open a web browser and navigate to https://github.com/pbfrandsen/fast_TIGER and click the 'Download ZIP'
+- Open your terminal application and enter the following commands:
+ - cd ~/Downloads
+ - unzip fast_TIGER-master.zip
+ - cd fast_TIGER-master
+ - make
+- Then you will want to copy your newly compiled program into the partitionfinder/programs directory
+ - To do this you can either open the fast_TIGER-master directory in finder and drag it into partitionfinder/programs, or you can enter the command: 'cp fast_TIGER <path_to_partitionfinder_directory>/programs' into your terminal window.
+
+fast_TIGER run:
+
+Now you are ready to run kmeans with fast_TIGER. To do so, set up the kmeans run as indicated in the manual and add '--kmeans fast_tiger' to your command.
+
+cython tiger:
+
+Pre-requisites:
+You should have a compiler installed. You can follow the instructions given for fast_TIGER to do this. You also need cython and the C++ boost library. Cython should be installed as part of the anaconda distribution. You can update it by typing 'conda update cython' in your terminal window.
+
+The easiest way to install the boost C++ library is to use homebrew. You can follow the directions on the homebrew website here (http://brew.sh). This involves issuing a single command to your terminal window and following the instructions.
+
+Restart your terminal window, then install boost by typing, 'brew install boost'. Once boost is installed you are ready to compile the cython version of tiger. You may need to add the path to your CFLAGS. Something like this might work:
+
+export CFLAGS="-I <path_to_include_dir>"
+
+The default path to the include dir is often /usr/local/include, so this might do it:
+
+export CFLAGS="-I /usr/local/include"
+
+
+Install:
+
+- Open a new terminal window and change directories into your partitionfinder directory. An easy way to find the path to the partitionfinder directory is to drag it from finder into your terminal window.
+ - cd <path_to_partitionfinder directory>
+- Then issue the following command:
+ - python setup.py
+- This should compile the cython version of tiger for you.
+
+cython tiger run:
+
+To run cython tiger, set up the kmeans run as described in the manual, then add '--kmeans tiger' to the command.
\ No newline at end of file
diff --git a/examples/README.txt b/examples/README.txt
new file mode 100644
index 0000000..b9ed44e
--- /dev/null
+++ b/examples/README.txt
@@ -0,0 +1,18 @@
+README for Examples
+___________________
+
+
+These folders contain two simple examples.
+
+The /nucleotide folder demonstrates PartitionFinder
+the /aminoacid folder demonstrates PartitionFinderProtein
+
+Instructions on how to run these examples are provided in the manual:
+
+For Mac Users: Page 7 of the manual
+For Windows Users: Page 9 of the manual
+
+Please email me if you have any questions.
+
+Rob Lanfear
+May 2012
\ No newline at end of file
diff --git a/examples/aminoacid/Als_etal_2004.phy b/examples/aminoacid/Als_etal_2004.phy
new file mode 100644
index 0000000..76d61e5
--- /dev/null
+++ b/examples/aminoacid/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/examples/aminoacid/partition_finder.cfg b/examples/aminoacid/partition_finder.cfg
new file mode 100644
index 0000000..d7e5df9
--- /dev/null
+++ b/examples/aminoacid/partition_finder.cfg
@@ -0,0 +1,23 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = aicc;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy | rcluster | hcluster | kmeans ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/examples/kmeans/partition_finder.cfg b/examples/kmeans/partition_finder.cfg
new file mode 100644
index 0000000..be376fc
--- /dev/null
+++ b/examples/kmeans/partition_finder.cfg
@@ -0,0 +1,19 @@
+## ALIGNMENT FILE ##
+alignment = test.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai <list> ##
+models = GTR, GTR+G, GTR+I+G;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = aicc;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+all = 1-7276;
+
+## SCHEMES, search: all | user | greedy | rcluster | hcluster | kmeans ##
+[schemes]
+search = kmeans;
diff --git a/examples/kmeans/test.phy b/examples/kmeans/test.phy
new file mode 100644
index 0000000..aa1cec1
--- /dev/null
+++ b/examples/kmeans/test.phy
@@ -0,0 +1,11 @@
+ 10 7276
+alvarezi AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACATAATTAAGCCTGTTTAAAAATGATCAATCTGACGAAAAA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTGTCGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTT----GACATTCATTGTTATGTTTTCAGCTTACTCACAACAAGTACTATTTTTATGCCCATAAT--TTAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAACTACTTACTAACTACAATAACTCATTATATTCAGATTATCAGAGTTTATTTATA-----GCGCTTTTT----------TTTTCTAATTTTGTGTAATTTTT-ATCAGA [...]
+andersi AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATGATCAACCTGACGAAAGA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTGTCGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGACATTCATTGTTATGTTTTCAGCTTCCTCACAA---GTACTATTTTTATGCCCATAAT--TTAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAATTACTTACTAACTACAATAACTCATTATATTCAGATTATCAGAGTTTATTTATA-----GCGCTTTTT--------TTTCCCCTAATTTTGTGTAATTTTTTATCAGAA [...]
+birchmanni AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATTATCAATCTGACGAAAAA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTGTTGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGACATTCATTGTTATGTTTTCAGCTTACTCACAA---GTACTATTTTTATGCCCATAAT--TTATT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAATTACTTACTAACCACAATAACTCATTATATTCAGATTATCAG--TTTATTTATA-----GCGCTTTTT---------TTTTTCTAATTTTGTGTAATTTTTTATCA [...]
+clemenciae AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACATAATTAAGCCTGTTTAAAAATGATCAATCTGACGAAAAA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTGTCGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTT----GACATTCATTGTTATGTTTTCAGCTTACTCACAACAAGTACTATTTTTATGCCCATAATATTTTATGCCCATAATTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAACTACTTACTAACTACAATAACTCATTATATTCAGATTATCAGAGTTTATTTATA-----GCACTTTTT---------TTTTTCTAATTTTGTGTAATTTTT-ATCA [...]
+continens AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATTATCAATCTGACGAAAAA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTATTGTTTGTACCTATTGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTATAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGACATTCATTGTTATGTTTTCAGCTTACTCACAA---GTACTATTTTTATGCCCATAAT--TTAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAATTACTTACTAACTACAATAACTCATTATATTCAGATGATCAGAGTTTATTTATA-----GCGCGTTTT---------TTTTTCTAATTTTGTGTAATTTTTTATCAG [...]
+cortezi AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATTATCAATCTGACGAAAAA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTATTGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTATAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGACATTCATTGTTATGTTTTCAGCTTACTCACAA---GTACTATTTTTATCCCCATAAT--TTAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAATTAC??????????????AACTCATTATATTCAGATTATCAGAGTTTATTTATA-----GCGCTTTTT---------TTTTTCTAATTTTGTGTAATTTTTTATCAGAA [...]
+couchianus AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATTATCAATCTGACAAAAGA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACTTGTTGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGACATTCATTGTTATGTTTCCAGCTTACTCACAACAAGTACGATTTTTATGCCCATAAT--TAAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCCTGTCAATTACTTACTAACTACAATAACTCATTATATTCAGATTATCAG--TTTATTTATA-----GCGCTTTTTT-------TTTTTTCTAATTTTGTGTAATTTTTTATCA [...]
+evelynae AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATGATCAACCTGACGAAAGA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTGTTGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGATATTCATTGTTATGTTTCCAGCTTACTCACAACAAGTACGATTTTTATGCCCATAAT--TAAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCCTGTCAATTACTTACTAACTACAATAACTCCTTATATTCAGATTATCAG--TTTATTTATA-----GCGCTTTTTT-------TTTTTTCTAATTTTGTGTAATTTTTTATCAGA [...]
+gordoni AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACAAAATTAAGCCTGTTTAAAAATTATCAATCTGACGAAAGA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACTTGTTGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTTAATTGACATTCATTGTTATGTTTCCAGCTTACTCACAACAAGTACGATTTTTATGCCCATAAT--TAAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCCTGTCAATTACTTACTAACTACAATAACTCATTATATTCAGATTATCAG--TTTATTTATA-----GCGCTTTTTT---------TTTTCTAATTTTGTGTAATTTTTTATCAGAA [...]
+hellerii AGATGCAACTTACAGCACTTGAGAAAAGTTTAAAATCTGACACAAGAAAAACATAATTAAGCCTGTTTAAAAATGATCAATCTGACGAAAAA----GAAACAGAACTTGTGACTTTTAAGTGCTGACACTTCTTTGGTTTTAAGTTTTTGTTTGTACCTGTCGTGGTTTGTGTGCACAGTGCATCTGCAGCTCAATCAATACACTTTAAATTCAAAATTAATTTTTGAAAATTAGAATTTTG-------TATTATAATTT----GACATTCATTGTTATGTTTTCAGCTTACTCACAACAAGTACTATTTTTATGCCCATAAT--TTAAT--------TTTTACTGTTTTTAAGAAAA--ATTACTCCTTGTCAACTACTTACTAACTACAATAACTCATTATATTCAGATTATCAGAGTTTATTTATA-----GCGCTTTTT----------TTTTCTAATTTTGTGTAATTTTT-ATCAGA [...]
diff --git a/examples/nucleotide/partition_finder.cfg b/examples/nucleotide/partition_finder.cfg
new file mode 100644
index 0000000..9a19717
--- /dev/null
+++ b/examples/nucleotide/partition_finder.cfg
@@ -0,0 +1,29 @@
+## ALIGNMENT FILE ##
+alignment = test.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION: all | allx | mrbayes | beast | gamma | gammai <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = aicc;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES, search: all | user | greedy | rcluster | hcluster | kmeans ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/examples/nucleotide/test.phy b/examples/nucleotide/test.phy
new file mode 100644
index 0000000..91e3c40
--- /dev/null
+++ b/examples/nucleotide/test.phy
@@ -0,0 +1,5 @@
+4 2208
+spp1 CTTGAGGTTCAGAATGGTAATGAA------GTGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCCATGGGTTCTTCCGACGGTCTGCGTCGCGGTCTGGATGTAAAAGACCTCGAGCACCCGATCGAAGTCCCAGTTGGTAAAGCAACACTGGGTCGTATCATGAACGTACTGGGTCAGCCAGTAGACATGAAGGGCGACATCGGTGAAGAAGAGCGTTGGGCT---------------ATCCACCGTGAAGCACCATCCTATGAAGAGCTGTCAAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTTGCGAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTTATTCGTAACATCGCGATCGAGCACTCCGGTTATTCTGTGTTTGCGGGCGTAGGTGAACGT [...]
+spp2 CTTGAGGTACAAAATGGTAATGAG------AGCCTGGTGCTGGAAGTTCAGCAGCAGCTCGGTGGTGGTATCGTACGTGCTATCGCCATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTTAAAGACCTTGAGCACCCGATCGAAGTCCCGGTTGGTAAAGCAACGCTGGGTCGTATCATGAACGTGCTGGGTCAGCCGATCGATATGAAAGGCGACATCGGCGAAGAAGAACGTTGGGCG---------------ATTCACCGTGCAGCACCTTCCTATGAAGAGCTCTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTCGCGAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTTGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAACACTCCGGTTACTCCGTGTTTGCTGGTGTTGGTGAGCGT [...]
+spp3 CTTGAGGTACAGAATAACAGCGAG------AAGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCAATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTGAAAGACCTCGAGCACCCGATCGAAGTCCCGGTAGGTAAAGCGACCCTGGGTCGTATCATGAACGTGCTGGGTCAGCCAATCGATATGAAAGGCGACATCGGCGAAGAAGATCGTTGGGCG---------------ATTCACCGCGCAGCACCTTCCTATGAAGAGCTGTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATTTGTCCGTTCGCTAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGCGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAGCACTCCGGTTACTCCGTGTTTGCAGGCGTGGGTGAGCGT [...]
+spp4 CTCGAGGTGAAAAATGGTGATGCT------CGTCTGGTGCTGGAAGTTCAGCAGCAGCTGGGTGGTGGCGTGGTTCGTACCATCGCCATGGGTACTTCTGACGGCCTGAAGCGCGGTCTGGAAGTTACCGACCTGAAAAAACCTATCCAGGTTCCGGTTGGTAAAGCAACCCTCGGCCGTATCATGAACGTATTGGGTGAGCCAATCGACATGAAAGGCGACCTGCAGAATGACGACGGCACTGTAGTAGAGGTTTCCTCTATTCACCGTGCAGCACCTTCGTATGAAGATCAGTCTAACTCGCAGGAACTGCTGGAAACCGGCATCAAGGTTATCGACCTGATGTGTCCGTTCGCTAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGGCTGAGCACTCAGGTTATTCGGTATTTGCTGGTGTGGGTGAGCGT [...]
diff --git a/partfinder/__init__.py b/partfinder/__init__.py
new file mode 100644
index 0000000..f5745ca
--- /dev/null
+++ b/partfinder/__init__.py
@@ -0,0 +1,16 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
diff --git a/partfinder/_tiger.cpp b/partfinder/_tiger.cpp
new file mode 100644
index 0000000..092214a
--- /dev/null
+++ b/partfinder/_tiger.cpp
@@ -0,0 +1,20553 @@
+/* Generated by Cython 0.21.1 */
+
+#define PY_SSIZE_T_CLEAN
+#ifndef CYTHON_USE_PYLONG_INTERNALS
+#ifdef PYLONG_BITS_IN_DIGIT
+#define CYTHON_USE_PYLONG_INTERNALS 0
+#else
+#include "pyconfig.h"
+#ifdef PYLONG_BITS_IN_DIGIT
+#define CYTHON_USE_PYLONG_INTERNALS 1
+#else
+#define CYTHON_USE_PYLONG_INTERNALS 0
+#endif
+#endif
+#endif
+#include "Python.h"
+#ifndef Py_PYTHON_H
+ #error Python headers needed to compile C extensions, please install development version of Python.
+#elif PY_VERSION_HEX < 0x02060000 || (0x03000000 <= PY_VERSION_HEX && PY_VERSION_HEX < 0x03020000)
+ #error Cython requires Python 2.6+ or Python 3.2+.
+#else
+#define CYTHON_ABI "0_21_1"
+#include <stddef.h>
+#ifndef offsetof
+#define offsetof(type, member) ( (size_t) & ((type*)0) -> member )
+#endif
+#if !defined(WIN32) && !defined(MS_WINDOWS)
+ #ifndef __stdcall
+ #define __stdcall
+ #endif
+ #ifndef __cdecl
+ #define __cdecl
+ #endif
+ #ifndef __fastcall
+ #define __fastcall
+ #endif
+#endif
+#ifndef DL_IMPORT
+ #define DL_IMPORT(t) t
+#endif
+#ifndef DL_EXPORT
+ #define DL_EXPORT(t) t
+#endif
+#ifndef PY_LONG_LONG
+ #define PY_LONG_LONG LONG_LONG
+#endif
+#ifndef Py_HUGE_VAL
+ #define Py_HUGE_VAL HUGE_VAL
+#endif
+#ifdef PYPY_VERSION
+#define CYTHON_COMPILING_IN_PYPY 1
+#define CYTHON_COMPILING_IN_CPYTHON 0
+#else
+#define CYTHON_COMPILING_IN_PYPY 0
+#define CYTHON_COMPILING_IN_CPYTHON 1
+#endif
+#if CYTHON_COMPILING_IN_PYPY && PY_VERSION_HEX < 0x02070600
+#define Py_OptimizeFlag 0
+#endif
+#define __PYX_BUILD_PY_SSIZE_T "n"
+#define CYTHON_FORMAT_SSIZE_T "z"
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_BUILTIN_MODULE_NAME "__builtin__"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a+k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyClass_Type
+#else
+ #define __Pyx_BUILTIN_MODULE_NAME "builtins"
+ #define __Pyx_PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos) \
+ PyCode_New(a, k, l, s, f, code, c, n, v, fv, cell, fn, name, fline, lnos)
+ #define __Pyx_DefaultClassType PyType_Type
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define Py_TPFLAGS_CHECKTYPES 0
+ #define Py_TPFLAGS_HAVE_INDEX 0
+ #define Py_TPFLAGS_HAVE_NEWBUFFER 0
+#endif
+#if PY_VERSION_HEX < 0x030400a1 && !defined(Py_TPFLAGS_HAVE_FINALIZE)
+ #define Py_TPFLAGS_HAVE_FINALIZE 0
+#endif
+#if PY_VERSION_HEX > 0x03030000 && defined(PyUnicode_KIND)
+ #define CYTHON_PEP393_ENABLED 1
+ #define __Pyx_PyUnicode_READY(op) (likely(PyUnicode_IS_READY(op)) ? \
+ 0 : _PyUnicode_Ready((PyObject *)(op)))
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_LENGTH(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) PyUnicode_READ_CHAR(u, i)
+ #define __Pyx_PyUnicode_KIND(u) PyUnicode_KIND(u)
+ #define __Pyx_PyUnicode_DATA(u) PyUnicode_DATA(u)
+ #define __Pyx_PyUnicode_READ(k, d, i) PyUnicode_READ(k, d, i)
+#else
+ #define CYTHON_PEP393_ENABLED 0
+ #define __Pyx_PyUnicode_READY(op) (0)
+ #define __Pyx_PyUnicode_GET_LENGTH(u) PyUnicode_GET_SIZE(u)
+ #define __Pyx_PyUnicode_READ_CHAR(u, i) ((Py_UCS4)(PyUnicode_AS_UNICODE(u)[i]))
+ #define __Pyx_PyUnicode_KIND(u) (sizeof(Py_UNICODE))
+ #define __Pyx_PyUnicode_DATA(u) ((void*)PyUnicode_AS_UNICODE(u))
+ #define __Pyx_PyUnicode_READ(k, d, i) ((void)(k), (Py_UCS4)(((Py_UNICODE*)d)[i]))
+#endif
+#if CYTHON_COMPILING_IN_PYPY
+ #define __Pyx_PyUnicode_Concat(a, b) PyNumber_Add(a, b)
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) PyNumber_Add(a, b)
+ #define __Pyx_PyFrozenSet_Size(s) PyObject_Size(s)
+#else
+ #define __Pyx_PyUnicode_Concat(a, b) PyUnicode_Concat(a, b)
+ #define __Pyx_PyUnicode_ConcatSafe(a, b) ((unlikely((a) == Py_None) || unlikely((b) == Py_None)) ? \
+ PyNumber_Add(a, b) : __Pyx_PyUnicode_Concat(a, b))
+ #define __Pyx_PyFrozenSet_Size(s) PySet_Size(s)
+#endif
+#define __Pyx_PyString_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : __Pyx_PyString_Format(a, b))
+#define __Pyx_PyUnicode_FormatSafe(a, b) ((unlikely((a) == Py_None)) ? PyNumber_Remainder(a, b) : PyUnicode_Format(a, b))
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyString_Format(a, b) PyUnicode_Format(a, b)
+#else
+ #define __Pyx_PyString_Format(a, b) PyString_Format(a, b)
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyBaseString_Type PyUnicode_Type
+ #define PyStringObject PyUnicodeObject
+ #define PyString_Type PyUnicode_Type
+ #define PyString_Check PyUnicode_Check
+ #define PyString_CheckExact PyUnicode_CheckExact
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyBaseString_Check(obj) PyUnicode_Check(obj)
+ #define __Pyx_PyBaseString_CheckExact(obj) PyUnicode_CheckExact(obj)
+#else
+ #define __Pyx_PyBaseString_Check(obj) (PyString_Check(obj) || PyUnicode_Check(obj))
+ #define __Pyx_PyBaseString_CheckExact(obj) (PyString_CheckExact(obj) || PyUnicode_CheckExact(obj))
+#endif
+#ifndef PySet_CheckExact
+ #define PySet_CheckExact(obj) (Py_TYPE(obj) == &PySet_Type)
+#endif
+#define __Pyx_TypeCheck(obj, type) PyObject_TypeCheck(obj, (PyTypeObject *)type)
+#if PY_MAJOR_VERSION >= 3
+ #define PyIntObject PyLongObject
+ #define PyInt_Type PyLong_Type
+ #define PyInt_Check(op) PyLong_Check(op)
+ #define PyInt_CheckExact(op) PyLong_CheckExact(op)
+ #define PyInt_FromString PyLong_FromString
+ #define PyInt_FromUnicode PyLong_FromUnicode
+ #define PyInt_FromLong PyLong_FromLong
+ #define PyInt_FromSize_t PyLong_FromSize_t
+ #define PyInt_FromSsize_t PyLong_FromSsize_t
+ #define PyInt_AsLong PyLong_AsLong
+ #define PyInt_AS_LONG PyLong_AS_LONG
+ #define PyInt_AsSsize_t PyLong_AsSsize_t
+ #define PyInt_AsUnsignedLongMask PyLong_AsUnsignedLongMask
+ #define PyInt_AsUnsignedLongLongMask PyLong_AsUnsignedLongLongMask
+ #define PyNumber_Int PyNumber_Long
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define PyBoolObject PyLongObject
+#endif
+#if PY_MAJOR_VERSION >= 3 && CYTHON_COMPILING_IN_PYPY
+ #ifndef PyUnicode_InternFromString
+ #define PyUnicode_InternFromString(s) PyUnicode_FromString(s)
+ #endif
+#endif
+#if PY_VERSION_HEX < 0x030200A4
+ typedef long Py_hash_t;
+ #define __Pyx_PyInt_FromHash_t PyInt_FromLong
+ #define __Pyx_PyInt_AsHash_t PyInt_AsLong
+#else
+ #define __Pyx_PyInt_FromHash_t PyInt_FromSsize_t
+ #define __Pyx_PyInt_AsHash_t PyInt_AsSsize_t
+#endif
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyMethod_New(func, self, klass) ((self) ? PyMethod_New(func, self) : PyInstanceMethod_New(func))
+#else
+ #define __Pyx_PyMethod_New(func, self, klass) PyMethod_New(func, self, klass)
+#endif
+#ifndef CYTHON_INLINE
+ #if defined(__GNUC__)
+ #define CYTHON_INLINE __inline__
+ #elif defined(_MSC_VER)
+ #define CYTHON_INLINE __inline
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_INLINE inline
+ #else
+ #define CYTHON_INLINE
+ #endif
+#endif
+#ifndef CYTHON_RESTRICT
+ #if defined(__GNUC__)
+ #define CYTHON_RESTRICT __restrict__
+ #elif defined(_MSC_VER) && _MSC_VER >= 1400
+ #define CYTHON_RESTRICT __restrict
+ #elif defined (__STDC_VERSION__) && __STDC_VERSION__ >= 199901L
+ #define CYTHON_RESTRICT restrict
+ #else
+ #define CYTHON_RESTRICT
+ #endif
+#endif
+#ifdef NAN
+#define __PYX_NAN() ((float) NAN)
+#else
+static CYTHON_INLINE float __PYX_NAN() {
+ /* Initialize NaN. The sign is irrelevant, an exponent with all bits 1 and
+ a nonzero mantissa means NaN. If the first bit in the mantissa is 1, it is
+ a quiet NaN. */
+ float value;
+ memset(&value, 0xFF, sizeof(value));
+ return value;
+}
+#endif
+#ifdef __cplusplus
+template<typename T>
+void __Pyx_call_destructor(T* x) {
+ x->~T();
+}
+#endif
+
+
+#if PY_MAJOR_VERSION >= 3
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_TrueDivide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceTrueDivide(x,y)
+#else
+ #define __Pyx_PyNumber_Divide(x,y) PyNumber_Divide(x,y)
+ #define __Pyx_PyNumber_InPlaceDivide(x,y) PyNumber_InPlaceDivide(x,y)
+#endif
+
+#ifndef __PYX_EXTERN_C
+ #ifdef __cplusplus
+ #define __PYX_EXTERN_C extern "C"
+ #else
+ #define __PYX_EXTERN_C extern
+ #endif
+#endif
+
+#if defined(WIN32) || defined(MS_WINDOWS)
+#define _USE_MATH_DEFINES
+#endif
+#include <math.h>
+#define __PYX_HAVE__partfinder___tiger
+#define __PYX_HAVE_API__partfinder___tiger
+#include <vector>
+#include "ios"
+#include "new"
+#include "stdexcept"
+#include "typeinfo"
+#include "string.h"
+#include <string>
+#include <boost/dynamic_bitset.hpp>
+#include "stdio.h"
+#include "stdlib.h"
+#include "numpy/arrayobject.h"
+#include "numpy/ufuncobject.h"
+#include "pythread.h"
+#include "pystate.h"
+#ifdef _OPENMP
+#include <omp.h>
+#endif /* _OPENMP */
+
+#ifdef PYREX_WITHOUT_ASSERTIONS
+#define CYTHON_WITHOUT_ASSERTIONS
+#endif
+
+#ifndef CYTHON_UNUSED
+# if defined(__GNUC__)
+# if !(defined(__cplusplus)) || (__GNUC__ > 3 || (__GNUC__ == 3 && __GNUC_MINOR__ >= 4))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+# elif defined(__ICC) || (defined(__INTEL_COMPILER) && !defined(_MSC_VER))
+# define CYTHON_UNUSED __attribute__ ((__unused__))
+# else
+# define CYTHON_UNUSED
+# endif
+#endif
+typedef struct {PyObject **p; char *s; const Py_ssize_t n; const char* encoding;
+ const char is_unicode; const char is_str; const char intern; } __Pyx_StringTabEntry;
+
+#define __PYX_DEFAULT_STRING_ENCODING_IS_ASCII 0
+#define __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT 0
+#define __PYX_DEFAULT_STRING_ENCODING ""
+#define __Pyx_PyObject_FromString __Pyx_PyBytes_FromString
+#define __Pyx_PyObject_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#define __Pyx_fits_Py_ssize_t(v, type, is_signed) ( \
+ (sizeof(type) < sizeof(Py_ssize_t)) || \
+ (sizeof(type) > sizeof(Py_ssize_t) && \
+ likely(v < (type)PY_SSIZE_T_MAX || \
+ v == (type)PY_SSIZE_T_MAX) && \
+ (!is_signed || likely(v > (type)PY_SSIZE_T_MIN || \
+ v == (type)PY_SSIZE_T_MIN))) || \
+ (sizeof(type) == sizeof(Py_ssize_t) && \
+ (is_signed || likely(v < (type)PY_SSIZE_T_MAX || \
+ v == (type)PY_SSIZE_T_MAX))) )
+static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject*);
+static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject*, Py_ssize_t* length);
+#define __Pyx_PyByteArray_FromString(s) PyByteArray_FromStringAndSize((const char*)s, strlen((const char*)s))
+#define __Pyx_PyByteArray_FromStringAndSize(s, l) PyByteArray_FromStringAndSize((const char*)s, l)
+#define __Pyx_PyBytes_FromString PyBytes_FromString
+#define __Pyx_PyBytes_FromStringAndSize PyBytes_FromStringAndSize
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char*);
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyStr_FromString __Pyx_PyBytes_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyBytes_FromStringAndSize
+#else
+ #define __Pyx_PyStr_FromString __Pyx_PyUnicode_FromString
+ #define __Pyx_PyStr_FromStringAndSize __Pyx_PyUnicode_FromStringAndSize
+#endif
+#define __Pyx_PyObject_AsSString(s) ((signed char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_AsUString(s) ((unsigned char*) __Pyx_PyObject_AsString(s))
+#define __Pyx_PyObject_FromUString(s) __Pyx_PyObject_FromString((const char*)s)
+#define __Pyx_PyBytes_FromUString(s) __Pyx_PyBytes_FromString((const char*)s)
+#define __Pyx_PyByteArray_FromUString(s) __Pyx_PyByteArray_FromString((const char*)s)
+#define __Pyx_PyStr_FromUString(s) __Pyx_PyStr_FromString((const char*)s)
+#define __Pyx_PyUnicode_FromUString(s) __Pyx_PyUnicode_FromString((const char*)s)
+#if PY_MAJOR_VERSION < 3
+static CYTHON_INLINE size_t __Pyx_Py_UNICODE_strlen(const Py_UNICODE *u)
+{
+ const Py_UNICODE *u_end = u;
+ while (*u_end++) ;
+ return (size_t)(u_end - u - 1);
+}
+#else
+#define __Pyx_Py_UNICODE_strlen Py_UNICODE_strlen
+#endif
+#define __Pyx_PyUnicode_FromUnicode(u) PyUnicode_FromUnicode(u, __Pyx_Py_UNICODE_strlen(u))
+#define __Pyx_PyUnicode_FromUnicodeAndLength PyUnicode_FromUnicode
+#define __Pyx_PyUnicode_AsUnicode PyUnicode_AsUnicode
+#define __Pyx_Owned_Py_None(b) (Py_INCREF(Py_None), Py_None)
+#define __Pyx_PyBool_FromLong(b) ((b) ? (Py_INCREF(Py_True), Py_True) : (Py_INCREF(Py_False), Py_False))
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject*);
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x);
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject*);
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t);
+#if CYTHON_COMPILING_IN_CPYTHON
+#define __pyx_PyFloat_AsDouble(x) (PyFloat_CheckExact(x) ? PyFloat_AS_DOUBLE(x) : PyFloat_AsDouble(x))
+#else
+#define __pyx_PyFloat_AsDouble(x) PyFloat_AsDouble(x)
+#endif
+#define __pyx_PyFloat_AsFloat(x) ((float) __pyx_PyFloat_AsDouble(x))
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+static int __Pyx_sys_getdefaultencoding_not_ascii;
+static int __Pyx_init_sys_getdefaultencoding_params(void) {
+ PyObject* sys;
+ PyObject* default_encoding = NULL;
+ PyObject* ascii_chars_u = NULL;
+ PyObject* ascii_chars_b = NULL;
+ const char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (!sys) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
+ Py_DECREF(sys);
+ if (!default_encoding) goto bad;
+ default_encoding_c = PyBytes_AsString(default_encoding);
+ if (!default_encoding_c) goto bad;
+ if (strcmp(default_encoding_c, "ascii") == 0) {
+ __Pyx_sys_getdefaultencoding_not_ascii = 0;
+ } else {
+ char ascii_chars[128];
+ int c;
+ for (c = 0; c < 128; c++) {
+ ascii_chars[c] = c;
+ }
+ __Pyx_sys_getdefaultencoding_not_ascii = 1;
+ ascii_chars_u = PyUnicode_DecodeASCII(ascii_chars, 128, NULL);
+ if (!ascii_chars_u) goto bad;
+ ascii_chars_b = PyUnicode_AsEncodedString(ascii_chars_u, default_encoding_c, NULL);
+ if (!ascii_chars_b || !PyBytes_Check(ascii_chars_b) || memcmp(ascii_chars, PyBytes_AS_STRING(ascii_chars_b), 128) != 0) {
+ PyErr_Format(
+ PyExc_ValueError,
+ "This module compiled with c_string_encoding=ascii, but default encoding '%.200s' is not a superset of ascii.",
+ default_encoding_c);
+ goto bad;
+ }
+ Py_DECREF(ascii_chars_u);
+ Py_DECREF(ascii_chars_b);
+ }
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(default_encoding);
+ Py_XDECREF(ascii_chars_u);
+ Py_XDECREF(ascii_chars_b);
+ return -1;
+}
+#endif
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT && PY_MAJOR_VERSION >= 3
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_DecodeUTF8(c_str, size, NULL)
+#else
+#define __Pyx_PyUnicode_FromStringAndSize(c_str, size) PyUnicode_Decode(c_str, size, __PYX_DEFAULT_STRING_ENCODING, NULL)
+#if __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+static char* __PYX_DEFAULT_STRING_ENCODING;
+static int __Pyx_init_sys_getdefaultencoding_params(void) {
+ PyObject* sys;
+ PyObject* default_encoding = NULL;
+ char* default_encoding_c;
+ sys = PyImport_ImportModule("sys");
+ if (!sys) goto bad;
+ default_encoding = PyObject_CallMethod(sys, (char*) (const char*) "getdefaultencoding", NULL);
+ Py_DECREF(sys);
+ if (!default_encoding) goto bad;
+ default_encoding_c = PyBytes_AsString(default_encoding);
+ if (!default_encoding_c) goto bad;
+ __PYX_DEFAULT_STRING_ENCODING = (char*) malloc(strlen(default_encoding_c));
+ if (!__PYX_DEFAULT_STRING_ENCODING) goto bad;
+ strcpy(__PYX_DEFAULT_STRING_ENCODING, default_encoding_c);
+ Py_DECREF(default_encoding);
+ return 0;
+bad:
+ Py_XDECREF(default_encoding);
+ return -1;
+}
+#endif
+#endif
+
+
+/* Test for GCC > 2.95 */
+#if defined(__GNUC__) && (__GNUC__ > 2 || (__GNUC__ == 2 && (__GNUC_MINOR__ > 95)))
+ #define likely(x) __builtin_expect(!!(x), 1)
+ #define unlikely(x) __builtin_expect(!!(x), 0)
+#else /* !__GNUC__ or GCC < 2.95 */
+ #define likely(x) (x)
+ #define unlikely(x) (x)
+#endif /* __GNUC__ */
+
+static PyObject *__pyx_m;
+static PyObject *__pyx_d;
+static PyObject *__pyx_b;
+static PyObject *__pyx_empty_tuple;
+static PyObject *__pyx_empty_bytes;
+static int __pyx_lineno;
+static int __pyx_clineno = 0;
+static const char * __pyx_cfilenm= __FILE__;
+static const char *__pyx_filename;
+
+#if !defined(CYTHON_CCOMPLEX)
+ #if defined(__cplusplus)
+ #define CYTHON_CCOMPLEX 1
+ #elif defined(_Complex_I)
+ #define CYTHON_CCOMPLEX 1
+ #else
+ #define CYTHON_CCOMPLEX 0
+ #endif
+#endif
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ #include <complex>
+ #else
+ #include <complex.h>
+ #endif
+#endif
+#if CYTHON_CCOMPLEX && !defined(__cplusplus) && defined(__sun__) && defined(__GNUC__)
+ #undef _Complex_I
+ #define _Complex_I 1.0fj
+#endif
+
+
+static const char *__pyx_f[] = {
+ "partfinder/_tiger.pyx",
+ "partfinder/_tiger.pxd",
+ "__init__.pxd",
+ "stringsource",
+ "type.pxd",
+};
+struct __pyx_memoryview_obj;
+typedef struct {
+ struct __pyx_memoryview_obj *memview;
+ char *data;
+ Py_ssize_t shape[8];
+ Py_ssize_t strides[8];
+ Py_ssize_t suboffsets[8];
+} __Pyx_memviewslice;
+
+#define IS_UNSIGNED(type) (((type) -1) > 0)
+struct __Pyx_StructField_;
+#define __PYX_BUF_FLAGS_PACKED_STRUCT (1 << 0)
+typedef struct {
+ const char* name;
+ struct __Pyx_StructField_* fields;
+ size_t size;
+ size_t arraysize[8];
+ int ndim;
+ char typegroup;
+ char is_unsigned;
+ int flags;
+} __Pyx_TypeInfo;
+typedef struct __Pyx_StructField_ {
+ __Pyx_TypeInfo* type;
+ const char* name;
+ size_t offset;
+} __Pyx_StructField;
+typedef struct {
+ __Pyx_StructField* field;
+ size_t parent_offset;
+} __Pyx_BufFmt_StackElem;
+typedef struct {
+ __Pyx_StructField root;
+ __Pyx_BufFmt_StackElem* head;
+ size_t fmt_offset;
+ size_t new_count, enc_count;
+ size_t struct_alignment;
+ int is_complex;
+ char enc_type;
+ char new_packmode;
+ char enc_packmode;
+ char is_valid_array;
+} __Pyx_BufFmt_Context;
+
+#include <pythread.h>
+#ifndef CYTHON_ATOMICS
+ #define CYTHON_ATOMICS 1
+#endif
+#define __pyx_atomic_int_type int
+#if CYTHON_ATOMICS && __GNUC__ >= 4 && (__GNUC_MINOR__ > 1 || \
+ (__GNUC_MINOR__ == 1 && __GNUC_PATCHLEVEL >= 2)) && \
+ !defined(__i386__)
+ #define __pyx_atomic_incr_aligned(value, lock) __sync_fetch_and_add(value, 1)
+ #define __pyx_atomic_decr_aligned(value, lock) __sync_fetch_and_sub(value, 1)
+ #ifdef __PYX_DEBUG_ATOMICS
+ #warning "Using GNU atomics"
+ #endif
+#elif CYTHON_ATOMICS && MSC_VER
+ #include <Windows.h>
+ #define __pyx_atomic_int_type LONG
+ #define __pyx_atomic_incr_aligned(value, lock) InterlockedIncrement(value)
+ #define __pyx_atomic_decr_aligned(value, lock) InterlockedDecrement(value)
+ #ifdef __PYX_DEBUG_ATOMICS
+ #warning "Using MSVC atomics"
+ #endif
+#elif CYTHON_ATOMICS && (defined(__ICC) || defined(__INTEL_COMPILER)) && 0
+ #define __pyx_atomic_incr_aligned(value, lock) _InterlockedIncrement(value)
+ #define __pyx_atomic_decr_aligned(value, lock) _InterlockedDecrement(value)
+ #ifdef __PYX_DEBUG_ATOMICS
+ #warning "Using Intel atomics"
+ #endif
+#else
+ #undef CYTHON_ATOMICS
+ #define CYTHON_ATOMICS 0
+ #ifdef __PYX_DEBUG_ATOMICS
+ #warning "Not using atomics"
+ #endif
+#endif
+typedef volatile __pyx_atomic_int_type __pyx_atomic_int;
+#if CYTHON_ATOMICS
+ #define __pyx_add_acquisition_count(memview) \
+ __pyx_atomic_incr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock)
+ #define __pyx_sub_acquisition_count(memview) \
+ __pyx_atomic_decr_aligned(__pyx_get_slice_count_pointer(memview), memview->lock)
+#else
+ #define __pyx_add_acquisition_count(memview) \
+ __pyx_add_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock)
+ #define __pyx_sub_acquisition_count(memview) \
+ __pyx_sub_acquisition_count_locked(__pyx_get_slice_count_pointer(memview), memview->lock)
+#endif
+
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":723
+ * # in Cython to enable them only on the right systems.
+ *
+ * ctypedef npy_int8 int8_t # <<<<<<<<<<<<<<
+ * ctypedef npy_int16 int16_t
+ * ctypedef npy_int32 int32_t
+ */
+typedef npy_int8 __pyx_t_5numpy_int8_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":724
+ *
+ * ctypedef npy_int8 int8_t
+ * ctypedef npy_int16 int16_t # <<<<<<<<<<<<<<
+ * ctypedef npy_int32 int32_t
+ * ctypedef npy_int64 int64_t
+ */
+typedef npy_int16 __pyx_t_5numpy_int16_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":725
+ * ctypedef npy_int8 int8_t
+ * ctypedef npy_int16 int16_t
+ * ctypedef npy_int32 int32_t # <<<<<<<<<<<<<<
+ * ctypedef npy_int64 int64_t
+ * #ctypedef npy_int96 int96_t
+ */
+typedef npy_int32 __pyx_t_5numpy_int32_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":726
+ * ctypedef npy_int16 int16_t
+ * ctypedef npy_int32 int32_t
+ * ctypedef npy_int64 int64_t # <<<<<<<<<<<<<<
+ * #ctypedef npy_int96 int96_t
+ * #ctypedef npy_int128 int128_t
+ */
+typedef npy_int64 __pyx_t_5numpy_int64_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":730
+ * #ctypedef npy_int128 int128_t
+ *
+ * ctypedef npy_uint8 uint8_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uint16 uint16_t
+ * ctypedef npy_uint32 uint32_t
+ */
+typedef npy_uint8 __pyx_t_5numpy_uint8_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":731
+ *
+ * ctypedef npy_uint8 uint8_t
+ * ctypedef npy_uint16 uint16_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uint32 uint32_t
+ * ctypedef npy_uint64 uint64_t
+ */
+typedef npy_uint16 __pyx_t_5numpy_uint16_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":732
+ * ctypedef npy_uint8 uint8_t
+ * ctypedef npy_uint16 uint16_t
+ * ctypedef npy_uint32 uint32_t # <<<<<<<<<<<<<<
+ * ctypedef npy_uint64 uint64_t
+ * #ctypedef npy_uint96 uint96_t
+ */
+typedef npy_uint32 __pyx_t_5numpy_uint32_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":733
+ * ctypedef npy_uint16 uint16_t
+ * ctypedef npy_uint32 uint32_t
+ * ctypedef npy_uint64 uint64_t # <<<<<<<<<<<<<<
+ * #ctypedef npy_uint96 uint96_t
+ * #ctypedef npy_uint128 uint128_t
+ */
+typedef npy_uint64 __pyx_t_5numpy_uint64_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":737
+ * #ctypedef npy_uint128 uint128_t
+ *
+ * ctypedef npy_float32 float32_t # <<<<<<<<<<<<<<
+ * ctypedef npy_float64 float64_t
+ * #ctypedef npy_float80 float80_t
+ */
+typedef npy_float32 __pyx_t_5numpy_float32_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":738
+ *
+ * ctypedef npy_float32 float32_t
+ * ctypedef npy_float64 float64_t # <<<<<<<<<<<<<<
+ * #ctypedef npy_float80 float80_t
+ * #ctypedef npy_float128 float128_t
+ */
+typedef npy_float64 __pyx_t_5numpy_float64_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":747
+ * # The int types are mapped a bit surprising --
+ * # numpy.int corresponds to 'l' and numpy.long to 'q'
+ * ctypedef npy_long int_t # <<<<<<<<<<<<<<
+ * ctypedef npy_longlong long_t
+ * ctypedef npy_longlong longlong_t
+ */
+typedef npy_long __pyx_t_5numpy_int_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":748
+ * # numpy.int corresponds to 'l' and numpy.long to 'q'
+ * ctypedef npy_long int_t
+ * ctypedef npy_longlong long_t # <<<<<<<<<<<<<<
+ * ctypedef npy_longlong longlong_t
+ *
+ */
+typedef npy_longlong __pyx_t_5numpy_long_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":749
+ * ctypedef npy_long int_t
+ * ctypedef npy_longlong long_t
+ * ctypedef npy_longlong longlong_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_ulong uint_t
+ */
+typedef npy_longlong __pyx_t_5numpy_longlong_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":751
+ * ctypedef npy_longlong longlong_t
+ *
+ * ctypedef npy_ulong uint_t # <<<<<<<<<<<<<<
+ * ctypedef npy_ulonglong ulong_t
+ * ctypedef npy_ulonglong ulonglong_t
+ */
+typedef npy_ulong __pyx_t_5numpy_uint_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":752
+ *
+ * ctypedef npy_ulong uint_t
+ * ctypedef npy_ulonglong ulong_t # <<<<<<<<<<<<<<
+ * ctypedef npy_ulonglong ulonglong_t
+ *
+ */
+typedef npy_ulonglong __pyx_t_5numpy_ulong_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":753
+ * ctypedef npy_ulong uint_t
+ * ctypedef npy_ulonglong ulong_t
+ * ctypedef npy_ulonglong ulonglong_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_intp intp_t
+ */
+typedef npy_ulonglong __pyx_t_5numpy_ulonglong_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":755
+ * ctypedef npy_ulonglong ulonglong_t
+ *
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+ * ctypedef npy_uintp uintp_t
+ *
+ */
+typedef npy_intp __pyx_t_5numpy_intp_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":756
+ *
+ * ctypedef npy_intp intp_t
+ * ctypedef npy_uintp uintp_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_double float_t
+ */
+typedef npy_uintp __pyx_t_5numpy_uintp_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":758
+ * ctypedef npy_uintp uintp_t
+ *
+ * ctypedef npy_double float_t # <<<<<<<<<<<<<<
+ * ctypedef npy_double double_t
+ * ctypedef npy_longdouble longdouble_t
+ */
+typedef npy_double __pyx_t_5numpy_float_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":759
+ *
+ * ctypedef npy_double float_t
+ * ctypedef npy_double double_t # <<<<<<<<<<<<<<
+ * ctypedef npy_longdouble longdouble_t
+ *
+ */
+typedef npy_double __pyx_t_5numpy_double_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":760
+ * ctypedef npy_double float_t
+ * ctypedef npy_double double_t
+ * ctypedef npy_longdouble longdouble_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_cfloat cfloat_t
+ */
+typedef npy_longdouble __pyx_t_5numpy_longdouble_t;
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ typedef ::std::complex< float > __pyx_t_float_complex;
+ #else
+ typedef float _Complex __pyx_t_float_complex;
+ #endif
+#else
+ typedef struct { float real, imag; } __pyx_t_float_complex;
+#endif
+
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ typedef ::std::complex< double > __pyx_t_double_complex;
+ #else
+ typedef double _Complex __pyx_t_double_complex;
+ #endif
+#else
+ typedef struct { double real, imag; } __pyx_t_double_complex;
+#endif
+
+
+/*--- Type declarations ---*/
+struct __pyx_obj_10partfinder_6_tiger_TigerBase;
+struct __pyx_obj_10partfinder_6_tiger_TigerDNA;
+struct __pyx_array_obj;
+struct __pyx_MemviewEnum_obj;
+struct __pyx_memoryview_obj;
+struct __pyx_memoryviewslice_obj;
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+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":762
+ * ctypedef npy_longdouble longdouble_t
+ *
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+ * ctypedef npy_cdouble cdouble_t
+ * ctypedef npy_clongdouble clongdouble_t
+ */
+typedef npy_cfloat __pyx_t_5numpy_cfloat_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":763
+ *
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+ * ctypedef npy_clongdouble clongdouble_t
+ *
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+typedef npy_cdouble __pyx_t_5numpy_cdouble_t;
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+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":764
+ * ctypedef npy_cfloat cfloat_t
+ * ctypedef npy_cdouble cdouble_t
+ * ctypedef npy_clongdouble clongdouble_t # <<<<<<<<<<<<<<
+ *
+ * ctypedef npy_cdouble complex_t
+ */
+typedef npy_clongdouble __pyx_t_5numpy_clongdouble_t;
+
+/* "../../anaconda/lib/python2.7/site-packages/Cython/Includes/numpy/__init__.pxd":766
+ * ctypedef npy_clongdouble clongdouble_t
+ *
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+ * cdef inline object PyArray_MultiIterNew1(a):
+ */
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+
+/* "partfinder/_tiger.pxd":32
+ * cdef void to_string(dynamic_bitset[size_t], string s)
+ *
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+ */
+typedef boost::dynamic_bitset<size_t> __pyx_t_10partfinder_6_tiger_c_Bitset;
+
+/* "partfinder/_tiger.pxd":33
+ *
+ * ctypedef dynamic_bitset[size_t] c_Bitset
+ * ctypedef vector[c_Bitset] c_ColumnBitsets # <<<<<<<<<<<<<<
+ * ctypedef vector[c_ColumnBitsets] c_AlignmentBitsets
+ *
+ */
+typedef std::vector<__pyx_t_10partfinder_6_tiger_c_Bitset> __pyx_t_10partfinder_6_tiger_c_ColumnBitsets;
+
+/* "partfinder/_tiger.pxd":34
+ * ctypedef dynamic_bitset[size_t] c_Bitset
+ * ctypedef vector[c_Bitset] c_ColumnBitsets
+ * ctypedef vector[c_ColumnBitsets] c_AlignmentBitsets # <<<<<<<<<<<<<<
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+typedef std::vector<__pyx_t_10partfinder_6_tiger_c_ColumnBitsets> __pyx_t_10partfinder_6_tiger_c_AlignmentBitsets;
+
+/* "partfinder/_tiger.pxd":36
+ * ctypedef vector[c_ColumnBitsets] c_AlignmentBitsets
+ *
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+ */
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+ PyObject_HEAD
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+ size_t species_count;
+ size_t column_count;
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+
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+ * return ret
+ *
+ * cdef class TigerDNA(TigerBase): # <<<<<<<<<<<<<<
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+ */
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+
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+ Py_ssize_t len;
+ char *format;
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+ Py_ssize_t *_shape;
+ Py_ssize_t *_strides;
+ Py_ssize_t itemsize;
+ PyObject *mode;
+ PyObject *_format;
+ void (*callback_free_data)(void *);
+ int free_data;
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+ PyObject *_size;
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+ __Pyx_memviewslice from_slice;
+ PyObject *from_object;
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+struct __pyx_vtabstruct_memoryview {
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+ PyObject *(*is_slice)(struct __pyx_memoryview_obj *, PyObject *);
+ PyObject *(*setitem_slice_assignment)(struct __pyx_memoryview_obj *, PyObject *, PyObject *);
+ PyObject *(*setitem_slice_assign_scalar)(struct __pyx_memoryview_obj *, struct __pyx_memoryview_obj *, PyObject *);
+ PyObject *(*setitem_indexed)(struct __pyx_memoryview_obj *, PyObject *, PyObject *);
+ PyObject *(*convert_item_to_object)(struct __pyx_memoryview_obj *, char *);
+ PyObject *(*assign_item_from_object)(struct __pyx_memoryview_obj *, char *, PyObject *);
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+/* "View.MemoryView":922
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+ * @cname('__pyx_memoryviewslice')
+ * cdef class _memoryviewslice(memoryview): # <<<<<<<<<<<<<<
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+struct __pyx_vtabstruct__memoryviewslice {
+ struct __pyx_vtabstruct_memoryview __pyx_base;
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+ void (*DECREF)(void*, PyObject*, int);
+ void (*GOTREF)(void*, PyObject*, int);
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+ #define __Pyx_GIVEREF(r)
+ #define __Pyx_XINCREF(r) Py_XINCREF(r)
+ #define __Pyx_XDECREF(r) Py_XDECREF(r)
+ #define __Pyx_XGOTREF(r)
+ #define __Pyx_XGIVEREF(r)
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+#define __Pyx_MEMVIEW_DIRECT 1
+#define __Pyx_MEMVIEW_PTR 2
+#define __Pyx_MEMVIEW_FULL 4
+#define __Pyx_MEMVIEW_CONTIG 8
+#define __Pyx_MEMVIEW_STRIDED 16
+#define __Pyx_MEMVIEW_FOLLOW 32
+#define __Pyx_IS_C_CONTIG 1
+#define __Pyx_IS_F_CONTIG 2
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+ __Pyx_memviewslice *memviewslice,
+ int memview_is_new_reference);
+static CYTHON_INLINE int __pyx_add_acquisition_count_locked(
+ __pyx_atomic_int *acquisition_count, PyThread_type_lock lock);
+static CYTHON_INLINE int __pyx_sub_acquisition_count_locked(
+ __pyx_atomic_int *acquisition_count, PyThread_type_lock lock);
+#define __pyx_get_slice_count_pointer(memview) (memview->acquisition_count_aligned_p)
+#define __pyx_get_slice_count(memview) (*__pyx_get_slice_count_pointer(memview))
+#define __PYX_INC_MEMVIEW(slice, have_gil) __Pyx_INC_MEMVIEW(slice, have_gil, __LINE__)
+#define __PYX_XDEC_MEMVIEW(slice, have_gil) __Pyx_XDEC_MEMVIEW(slice, have_gil, __LINE__)
+static CYTHON_INLINE void __Pyx_INC_MEMVIEW(__Pyx_memviewslice *, int, int);
+static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *, int, int);
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected);
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index);
+
+static CYTHON_INLINE int __Pyx_IterFinish(void);
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected);
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb);
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb);
+
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause);
+
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void);
+
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type);
+
+static void __Pyx_RaiseDoubleKeywordsError(const char* func_name, PyObject* kw_name);
+
+static int __Pyx_ParseOptionalKeywords(PyObject *kwds, PyObject **argnames[], \
+ PyObject *kwds2, PyObject *values[], Py_ssize_t num_pos_args, \
+ const char* function_name);
+
+static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
+ const char *name, int exact);
+
+#include <string.h>
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals);
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals);
+
+#if PY_MAJOR_VERSION >= 3
+#define __Pyx_PyString_Equals __Pyx_PyUnicode_Equals
+#else
+#define __Pyx_PyString_Equals __Pyx_PyBytes_Equals
+#endif
+
+#ifndef __PYX_FORCE_INIT_THREADS
+ #define __PYX_FORCE_INIT_THREADS 0
+#endif
+
+#define UNARY_NEG_WOULD_OVERFLOW(x) (((x) < 0) & ((unsigned long)(x) == 0-(unsigned long)(x)))
+
+static CYTHON_UNUSED int __pyx_array_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/
+static PyObject *get_memview(PyObject *__pyx_v_self); /*proto*/
+static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *, PyObject *);
+
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors));
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb);
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb);
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb);
+
+static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb);
+
+#define __Pyx_GetItemInt(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
+ __Pyx_GetItemInt_Fast(o, (Py_ssize_t)i, is_list, wraparound, boundscheck) : \
+ (is_list ? (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL) : \
+ __Pyx_GetItemInt_Generic(o, to_py_func(i))))
+#define __Pyx_GetItemInt_List(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
+ __Pyx_GetItemInt_List_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
+ (PyErr_SetString(PyExc_IndexError, "list index out of range"), (PyObject*)NULL))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+#define __Pyx_GetItemInt_Tuple(o, i, type, is_signed, to_py_func, is_list, wraparound, boundscheck) \
+ (__Pyx_fits_Py_ssize_t(i, type, is_signed) ? \
+ __Pyx_GetItemInt_Tuple_Fast(o, (Py_ssize_t)i, wraparound, boundscheck) : \
+ (PyErr_SetString(PyExc_IndexError, "tuple index out of range"), (PyObject*)NULL))
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j);
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck);
+
+static CYTHON_UNUSED int __pyx_memoryview_getbuffer(PyObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /*proto*/
+static PyObject *__pyx_memoryview_transpose(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview__get__base(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview_get_shape(PyObject *__pyx_v_self); /*proto*/
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_ListComp_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len)) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
+ }
+ return PyList_Append(list, x);
+}
+#else
+#define __Pyx_ListComp_Append(L,x) PyList_Append(L,x)
+#endif
+
+static PyObject *__pyx_memoryview_get_strides(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview_get_suboffsets(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview_get_ndim(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview_get_itemsize(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview_get_nbytes(PyObject *__pyx_v_self); /*proto*/
+static PyObject *__pyx_memoryview_get_size(PyObject *__pyx_v_self); /*proto*/
+static CYTHON_INLINE int __Pyx_PyList_Extend(PyObject* L, PyObject* v) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject* none = _PyList_Extend((PyListObject*)L, v);
+ if (unlikely(!none))
+ return -1;
+ Py_DECREF(none);
+ return 0;
+#else
+ return PyList_SetSlice(L, PY_SSIZE_T_MAX, PY_SSIZE_T_MAX, v);
+#endif
+}
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE int __Pyx_PyList_Append(PyObject* list, PyObject* x) {
+ PyListObject* L = (PyListObject*) list;
+ Py_ssize_t len = Py_SIZE(list);
+ if (likely(L->allocated > len) & likely(len > (L->allocated >> 1))) {
+ Py_INCREF(x);
+ PyList_SET_ITEM(list, len, x);
+ Py_SIZE(list) = len+1;
+ return 0;
+ }
+ return PyList_Append(list, x);
+}
+#else
+#define __Pyx_PyList_Append(L,x) PyList_Append(L,x)
+#endif
+
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname);
+
+static PyObject *__pyx_memoryviewslice__get__base(PyObject *__pyx_v_self); /*proto*/
+static void __Pyx_WriteUnraisable(const char *name, int clineno,
+ int lineno, const char *filename,
+ int full_traceback);
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg);
+#endif
+
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg);
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable);
+
+typedef struct {
+ int code_line;
+ PyCodeObject* code_object;
+} __Pyx_CodeObjectCacheEntry;
+struct __Pyx_CodeObjectCache {
+ int count;
+ int max_count;
+ __Pyx_CodeObjectCacheEntry* entries;
+};
+static struct __Pyx_CodeObjectCache __pyx_code_cache = {0,0,NULL};
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line);
+static PyCodeObject *__pyx_find_code_object(int code_line);
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object);
+
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename);
+
+#include <new>
+
+typedef struct {
+ Py_ssize_t shape, strides, suboffsets;
+} __Pyx_Buf_DimInfo;
+typedef struct {
+ size_t refcount;
+ Py_buffer pybuffer;
+} __Pyx_Buffer;
+typedef struct {
+ __Pyx_Buffer *rcbuffer;
+ char *data;
+ __Pyx_Buf_DimInfo diminfo[8];
+} __Pyx_LocalBuf_ND;
+
+#if PY_MAJOR_VERSION < 3
+ static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags);
+ static void __Pyx_ReleaseBuffer(Py_buffer *view);
+#else
+ #define __Pyx_GetBuffer PyObject_GetBuffer
+ #define __Pyx_ReleaseBuffer PyBuffer_Release
+#endif
+
+
+static Py_ssize_t __Pyx_zeros[] = {0, 0, 0, 0, 0, 0, 0, 0};
+static Py_ssize_t __Pyx_minusones[] = {-1, -1, -1, -1, -1, -1, -1, -1};
+
+static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level);
+
+static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *);
+
+#ifndef __Pyx_CppExn2PyErr
+#include <new>
+#include <typeinfo>
+#include <stdexcept>
+#include <ios>
+static void __Pyx_CppExn2PyErr() {
+ try {
+ if (PyErr_Occurred())
+ ; // let the latest Python exn pass through and ignore the current one
+ else
+ throw;
+ } catch (const std::bad_alloc& exn) {
+ PyErr_SetString(PyExc_MemoryError, exn.what());
+ } catch (const std::bad_cast& exn) {
+ PyErr_SetString(PyExc_TypeError, exn.what());
+ } catch (const std::domain_error& exn) {
+ PyErr_SetString(PyExc_ValueError, exn.what());
+ } catch (const std::invalid_argument& exn) {
+ PyErr_SetString(PyExc_ValueError, exn.what());
+ } catch (const std::ios_base::failure& exn) {
+ PyErr_SetString(PyExc_IOError, exn.what());
+ } catch (const std::out_of_range& exn) {
+ PyErr_SetString(PyExc_IndexError, exn.what());
+ } catch (const std::overflow_error& exn) {
+ PyErr_SetString(PyExc_OverflowError, exn.what());
+ } catch (const std::range_error& exn) {
+ PyErr_SetString(PyExc_ArithmeticError, exn.what());
+ } catch (const std::underflow_error& exn) {
+ PyErr_SetString(PyExc_ArithmeticError, exn.what());
+ } catch (const std::exception& exn) {
+ PyErr_SetString(PyExc_RuntimeError, exn.what());
+ }
+ catch (...)
+ {
+ PyErr_SetString(PyExc_RuntimeError, "Unknown exception");
+ }
+}
+#endif
+
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ #define __Pyx_CREAL(z) ((z).real())
+ #define __Pyx_CIMAG(z) ((z).imag())
+ #else
+ #define __Pyx_CREAL(z) (__real__(z))
+ #define __Pyx_CIMAG(z) (__imag__(z))
+ #endif
+#else
+ #define __Pyx_CREAL(z) ((z).real)
+ #define __Pyx_CIMAG(z) ((z).imag)
+#endif
+#if (defined(_WIN32) || defined(__clang__)) && defined(__cplusplus) && CYTHON_CCOMPLEX
+ #define __Pyx_SET_CREAL(z,x) ((z).real(x))
+ #define __Pyx_SET_CIMAG(z,y) ((z).imag(y))
+#else
+ #define __Pyx_SET_CREAL(z,x) __Pyx_CREAL(z) = (x)
+ #define __Pyx_SET_CIMAG(z,y) __Pyx_CIMAG(z) = (y)
+#endif
+
+static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float, float);
+
+#if CYTHON_CCOMPLEX
+ #define __Pyx_c_eqf(a, b) ((a)==(b))
+ #define __Pyx_c_sumf(a, b) ((a)+(b))
+ #define __Pyx_c_difff(a, b) ((a)-(b))
+ #define __Pyx_c_prodf(a, b) ((a)*(b))
+ #define __Pyx_c_quotf(a, b) ((a)/(b))
+ #define __Pyx_c_negf(a) (-(a))
+ #ifdef __cplusplus
+ #define __Pyx_c_is_zerof(z) ((z)==(float)0)
+ #define __Pyx_c_conjf(z) (::std::conj(z))
+ #if 1
+ #define __Pyx_c_absf(z) (::std::abs(z))
+ #define __Pyx_c_powf(a, b) (::std::pow(a, b))
+ #endif
+ #else
+ #define __Pyx_c_is_zerof(z) ((z)==0)
+ #define __Pyx_c_conjf(z) (conjf(z))
+ #if 1
+ #define __Pyx_c_absf(z) (cabsf(z))
+ #define __Pyx_c_powf(a, b) (cpowf(a, b))
+ #endif
+ #endif
+#else
+ static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex, __pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex);
+ #if 1
+ static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex);
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex, __pyx_t_float_complex);
+ #endif
+#endif
+
+static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double, double);
+
+#if CYTHON_CCOMPLEX
+ #define __Pyx_c_eq(a, b) ((a)==(b))
+ #define __Pyx_c_sum(a, b) ((a)+(b))
+ #define __Pyx_c_diff(a, b) ((a)-(b))
+ #define __Pyx_c_prod(a, b) ((a)*(b))
+ #define __Pyx_c_quot(a, b) ((a)/(b))
+ #define __Pyx_c_neg(a) (-(a))
+ #ifdef __cplusplus
+ #define __Pyx_c_is_zero(z) ((z)==(double)0)
+ #define __Pyx_c_conj(z) (::std::conj(z))
+ #if 1
+ #define __Pyx_c_abs(z) (::std::abs(z))
+ #define __Pyx_c_pow(a, b) (::std::pow(a, b))
+ #endif
+ #else
+ #define __Pyx_c_is_zero(z) ((z)==0)
+ #define __Pyx_c_conj(z) (conj(z))
+ #if 1
+ #define __Pyx_c_abs(z) (cabs(z))
+ #define __Pyx_c_pow(a, b) (cpow(a, b))
+ #endif
+ #endif
+#else
+ static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex, __pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex);
+ static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex);
+ #if 1
+ static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex);
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex, __pyx_t_double_complex);
+ #endif
+#endif
+
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value);
+
+static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *);
+
+static int __pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs,
+ char order, int ndim);
+
+static int __pyx_slices_overlap(__Pyx_memviewslice *slice1,
+ __Pyx_memviewslice *slice2,
+ int ndim, size_t itemsize);
+
+static __Pyx_memviewslice
+__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs,
+ const char *mode, int ndim,
+ size_t sizeof_dtype, int contig_flag,
+ int dtype_is_object);
+
+static CYTHON_INLINE PyObject *__pyx_capsule_create(void *p, const char *sig);
+
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value);
+
+static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *);
+
+static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *);
+
+static int __pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b);
+
+static int __Pyx_ValidateAndInit_memviewslice(
+ int *axes_specs,
+ int c_or_f_flag,
+ int buf_flags,
+ int ndim,
+ __Pyx_TypeInfo *dtype,
+ __Pyx_BufFmt_StackElem stack[],
+ __Pyx_memviewslice *memviewslice,
+ PyObject *original_obj);
+
+static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn_npy_double(PyObject *);
+
+static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsdsds_nn_npy_uint8(PyObject *);
+
+static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn_npy_uint8(PyObject *);
+
+static int __Pyx_check_binary_version(void);
+
+#if !defined(__Pyx_PyIdentifier_FromString)
+#if PY_MAJOR_VERSION < 3
+ #define __Pyx_PyIdentifier_FromString(s) PyString_FromString(s)
+#else
+ #define __Pyx_PyIdentifier_FromString(s) PyUnicode_FromString(s)
+#endif
+#endif
+
+static PyObject *__Pyx_ImportModule(const char *name);
+
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name, size_t size, int strict);
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t);
+
+static char *__pyx_memoryview_get_item_pointer(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto*/
+static PyObject *__pyx_memoryview_is_slice(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj); /* proto*/
+static PyObject *__pyx_memoryview_setitem_slice_assignment(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_dst, PyObject *__pyx_v_src); /* proto*/
+static PyObject *__pyx_memoryview_setitem_slice_assign_scalar(struct __pyx_memoryview_obj *__pyx_v_self, struct __pyx_memoryview_obj *__pyx_v_dst, PyObject *__pyx_v_value); /* proto*/
+static PyObject *__pyx_memoryview_setitem_indexed(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto*/
+static PyObject *__pyx_memoryview_convert_item_to_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/
+static PyObject *__pyx_memoryview_assign_item_from_object(struct __pyx_memoryview_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/
+static PyObject *__pyx_memoryviewslice_convert_item_to_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp); /* proto*/
+static PyObject *__pyx_memoryviewslice_assign_item_from_object(struct __pyx_memoryviewslice_obj *__pyx_v_self, char *__pyx_v_itemp, PyObject *__pyx_v_value); /* proto*/
+
+/* Module declarations from 'libcpp.vector' */
+
+/* Module declarations from 'libc.string' */
+
+/* Module declarations from 'libcpp.string' */
+
+/* Module declarations from 'cpython.buffer' */
+
+/* Module declarations from 'cpython.ref' */
+
+/* Module declarations from 'libc.stdio' */
+
+/* Module declarations from 'cpython.object' */
+
+/* Module declarations from '__builtin__' */
+
+/* Module declarations from 'cpython.type' */
+static PyTypeObject *__pyx_ptype_7cpython_4type_type = 0;
+
+/* Module declarations from 'libc.stdlib' */
+
+/* Module declarations from 'numpy' */
+
+/* Module declarations from 'numpy' */
+static PyTypeObject *__pyx_ptype_5numpy_dtype = 0;
+static PyTypeObject *__pyx_ptype_5numpy_flatiter = 0;
+static PyTypeObject *__pyx_ptype_5numpy_broadcast = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ndarray = 0;
+static PyTypeObject *__pyx_ptype_5numpy_ufunc = 0;
+static CYTHON_INLINE char *__pyx_f_5numpy__util_dtypestring(PyArray_Descr *, char *, char *, int *); /*proto*/
+
+/* Module declarations from 'cython.view' */
+
+/* Module declarations from 'cython' */
+
+/* Module declarations from 'partfinder._tiger' */
+static PyTypeObject *__pyx_ptype_10partfinder_6_tiger_TigerBase = 0;
+static PyTypeObject *__pyx_ptype_10partfinder_6_tiger_TigerDNA = 0;
+static PyTypeObject *__pyx_array_type = 0;
+static PyTypeObject *__pyx_MemviewEnum_type = 0;
+static PyTypeObject *__pyx_memoryview_type = 0;
+static PyTypeObject *__pyx_memoryviewslice_type = 0;
+static PyObject *generic = 0;
+static PyObject *strided = 0;
+static PyObject *indirect = 0;
+static PyObject *contiguous = 0;
+static PyObject *indirect_contiguous = 0;
+static struct __pyx_array_obj *__pyx_array_new(PyObject *, Py_ssize_t, char *, char *, char *); /*proto*/
+static void *__pyx_align_pointer(void *, size_t); /*proto*/
+static PyObject *__pyx_memoryview_new(PyObject *, int, int, __Pyx_TypeInfo *); /*proto*/
+static CYTHON_INLINE int __pyx_memoryview_check(PyObject *); /*proto*/
+static PyObject *_unellipsify(PyObject *, int); /*proto*/
+static PyObject *assert_direct_dimensions(Py_ssize_t *, int); /*proto*/
+static struct __pyx_memoryview_obj *__pyx_memview_slice(struct __pyx_memoryview_obj *, PyObject *); /*proto*/
+static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int *, Py_ssize_t, Py_ssize_t, Py_ssize_t, int, int, int, int); /*proto*/
+static char *__pyx_pybuffer_index(Py_buffer *, char *, Py_ssize_t, Py_ssize_t); /*proto*/
+static int __pyx_memslice_transpose(__Pyx_memviewslice *); /*proto*/
+static PyObject *__pyx_memoryview_fromslice(__Pyx_memviewslice, int, PyObject *(*)(char *), int (*)(char *, PyObject *), int); /*proto*/
+static __Pyx_memviewslice *__pyx_memoryview_get_slice_from_memoryview(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/
+static void __pyx_memoryview_slice_copy(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/
+static PyObject *__pyx_memoryview_copy_object(struct __pyx_memoryview_obj *); /*proto*/
+static PyObject *__pyx_memoryview_copy_object_from_slice(struct __pyx_memoryview_obj *, __Pyx_memviewslice *); /*proto*/
+static Py_ssize_t abs_py_ssize_t(Py_ssize_t); /*proto*/
+static char __pyx_get_best_slice_order(__Pyx_memviewslice *, int); /*proto*/
+static void _copy_strided_to_strided(char *, Py_ssize_t *, char *, Py_ssize_t *, Py_ssize_t *, Py_ssize_t *, int, size_t); /*proto*/
+static void copy_strided_to_strided(__Pyx_memviewslice *, __Pyx_memviewslice *, int, size_t); /*proto*/
+static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *, int); /*proto*/
+static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *, Py_ssize_t *, Py_ssize_t, int, char); /*proto*/
+static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *, __Pyx_memviewslice *, char, int); /*proto*/
+static int __pyx_memoryview_err_extents(int, Py_ssize_t, Py_ssize_t); /*proto*/
+static int __pyx_memoryview_err_dim(PyObject *, char *, int); /*proto*/
+static int __pyx_memoryview_err(PyObject *, char *); /*proto*/
+static int __pyx_memoryview_copy_contents(__Pyx_memviewslice, __Pyx_memviewslice, int, int, int); /*proto*/
+static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *, int, int); /*proto*/
+static void __pyx_memoryview_refcount_copying(__Pyx_memviewslice *, int, int, int); /*proto*/
+static void __pyx_memoryview_refcount_objects_in_slice_with_gil(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/
+static void __pyx_memoryview_refcount_objects_in_slice(char *, Py_ssize_t *, Py_ssize_t *, int, int); /*proto*/
+static void __pyx_memoryview_slice_assign_scalar(__Pyx_memviewslice *, int, size_t, void *, int); /*proto*/
+static void __pyx_memoryview__slice_assign_scalar(char *, Py_ssize_t *, Py_ssize_t *, int, size_t, void *); /*proto*/
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_double = { "npy_double", NULL, sizeof(npy_double), { 0 }, 0, 'R', 0, 0 };
+static __Pyx_TypeInfo __Pyx_TypeInfo_nn_npy_uint8 = { "npy_uint8", NULL, sizeof(npy_uint8), { 0 }, 0, IS_UNSIGNED(npy_uint8) ? 'U' : 'I', IS_UNSIGNED(npy_uint8), 0 };
+#define __Pyx_MODULE_NAME "partfinder._tiger"
+int __pyx_module_is_main_partfinder___tiger = 0;
+
+/* Implementation of 'partfinder._tiger' */
+static PyObject *__pyx_builtin_range;
+static PyObject *__pyx_builtin_ValueError;
+static PyObject *__pyx_builtin_RuntimeError;
+static PyObject *__pyx_builtin_MemoryError;
+static PyObject *__pyx_builtin_enumerate;
+static PyObject *__pyx_builtin_Ellipsis;
+static PyObject *__pyx_builtin_TypeError;
+static PyObject *__pyx_builtin_xrange;
+static PyObject *__pyx_builtin_id;
+static PyObject *__pyx_builtin_IndexError;
+static int __pyx_pf_10partfinder_6_tiger_9TigerBase___cinit__(CYTHON_UNUSED struct __pyx_obj_10partfinder_6_tiger_TigerBase *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_10partfinder_6_tiger_9TigerBase_2calc_rates(struct __pyx_obj_10partfinder_6_tiger_TigerBase *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_10partfinder_6_tiger_9TigerBase_4bitsets_as_array(struct __pyx_obj_10partfinder_6_tiger_TigerBase *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_10partfinder_6_tiger_9TigerBase_13species_count___get__(struct __pyx_obj_10partfinder_6_tiger_TigerBase *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_10partfinder_6_tiger_9TigerBase_12column_count___get__(struct __pyx_obj_10partfinder_6_tiger_TigerBase *__pyx_v_self); /* proto */
+static int __pyx_pf_10partfinder_6_tiger_8TigerDNA___cinit__(struct __pyx_obj_10partfinder_6_tiger_TigerDNA *__pyx_v_self); /* proto */
+static PyObject *__pyx_pf_10partfinder_6_tiger_8TigerDNA_2build_bitsets(struct __pyx_obj_10partfinder_6_tiger_TigerDNA *__pyx_v_self, PyObject *__pyx_v_alignment); /* proto */
+static int __pyx_pf_5numpy_7ndarray___getbuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
+static void __pyx_pf_5numpy_7ndarray_2__releasebuffer__(PyArrayObject *__pyx_v_self, Py_buffer *__pyx_v_info); /* proto */
+static int __pyx_array_MemoryView_5array___cinit__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_shape, Py_ssize_t __pyx_v_itemsize, PyObject *__pyx_v_format, PyObject *__pyx_v_mode, int __pyx_v_allocate_buffer); /* proto */
+static int __pyx_array_getbuffer_MemoryView_5array_2__getbuffer__(struct __pyx_array_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
+static void __pyx_array_MemoryView_5array_4__dealloc__(struct __pyx_array_obj *__pyx_v_self); /* proto */
+static PyObject *get_memview_MemoryView_5array_7memview___get__(struct __pyx_array_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_array_MemoryView_5array_6__getattr__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_attr); /* proto */
+static PyObject *__pyx_array_MemoryView_5array_8__getitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item); /* proto */
+static int __pyx_array_MemoryView_5array_10__setitem__(struct __pyx_array_obj *__pyx_v_self, PyObject *__pyx_v_item, PyObject *__pyx_v_value); /* proto */
+static int __pyx_MemviewEnum_MemoryView_4Enum___init__(struct __pyx_MemviewEnum_obj *__pyx_v_self, PyObject *__pyx_v_name); /* proto */
+static PyObject *__pyx_MemviewEnum_MemoryView_4Enum_2__repr__(struct __pyx_MemviewEnum_obj *__pyx_v_self); /* proto */
+static int __pyx_memoryview_MemoryView_10memoryview___cinit__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_obj, int __pyx_v_flags, int __pyx_v_dtype_is_object); /* proto */
+static void __pyx_memoryview_MemoryView_10memoryview_2__dealloc__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_4__getitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index); /* proto */
+static int __pyx_memoryview_MemoryView_10memoryview_6__setitem__(struct __pyx_memoryview_obj *__pyx_v_self, PyObject *__pyx_v_index, PyObject *__pyx_v_value); /* proto */
+static int __pyx_memoryview_getbuffer_MemoryView_10memoryview_8__getbuffer__(struct __pyx_memoryview_obj *__pyx_v_self, Py_buffer *__pyx_v_info, int __pyx_v_flags); /* proto */
+static PyObject *__pyx_memoryview_transpose_MemoryView_10memoryview_1T___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview__get__base_MemoryView_10memoryview_4base___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_shape_MemoryView_10memoryview_5shape___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_strides_MemoryView_10memoryview_7strides___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_suboffsets_MemoryView_10memoryview_10suboffsets___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_ndim_MemoryView_10memoryview_4ndim___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_itemsize_MemoryView_10memoryview_8itemsize___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_nbytes_MemoryView_10memoryview_6nbytes___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_get_size_MemoryView_10memoryview_4size___get__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static Py_ssize_t __pyx_memoryview_MemoryView_10memoryview_10__len__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_12__repr__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_14__str__(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_16is_c_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_18is_f_contig(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_20copy(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryview_MemoryView_10memoryview_22copy_fortran(struct __pyx_memoryview_obj *__pyx_v_self); /* proto */
+static void __pyx_memoryviewslice_MemoryView_16_memoryviewslice___dealloc__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_memoryviewslice__get__base_MemoryView_16_memoryviewslice_4base___get__(struct __pyx_memoryviewslice_obj *__pyx_v_self); /* proto */
+static PyObject *__pyx_tp_new_10partfinder_6_tiger_TigerBase(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_10partfinder_6_tiger_TigerDNA(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k); /*proto*/
+static char __pyx_k_B[] = "B";
+static char __pyx_k_H[] = "H";
+static char __pyx_k_I[] = "I";
+static char __pyx_k_L[] = "L";
+static char __pyx_k_O[] = "O";
+static char __pyx_k_Q[] = "Q";
+static char __pyx_k_b[] = "b";
+static char __pyx_k_c[] = "c";
+static char __pyx_k_d[] = "d";
+static char __pyx_k_f[] = "f";
+static char __pyx_k_g[] = "g";
+static char __pyx_k_h[] = "h";
+static char __pyx_k_i[] = "i";
+static char __pyx_k_l[] = "l";
+static char __pyx_k_q[] = "q";
+static char __pyx_k_Zd[] = "Zd";
+static char __pyx_k_Zf[] = "Zf";
+static char __pyx_k_Zg[] = "Zg";
+static char __pyx_k_f8[] = "f8";
+static char __pyx_k_id[] = "id";
+static char __pyx_k_u1[] = "u1";
+static char __pyx_k_obj[] = "obj";
+static char __pyx_k_sys[] = "sys";
+static char __pyx_k_base[] = "base";
+static char __pyx_k_copy[] = "copy";
+static char __pyx_k_data[] = "data";
+static char __pyx_k_main[] = "__main__";
+static char __pyx_k_mode[] = "mode";
+static char __pyx_k_name[] = "name";
+static char __pyx_k_ndim[] = "ndim";
+static char __pyx_k_pack[] = "pack";
+static char __pyx_k_size[] = "size";
+static char __pyx_k_step[] = "step";
+static char __pyx_k_stop[] = "stop";
+static char __pyx_k_test[] = "__test__";
+static char __pyx_k_class[] = "__class__";
+static char __pyx_k_dtype[] = "dtype";
+static char __pyx_k_error[] = "error";
+static char __pyx_k_flags[] = "flags";
+static char __pyx_k_numpy[] = "numpy";
+static char __pyx_k_range[] = "range";
+static char __pyx_k_shape[] = "shape";
+static char __pyx_k_start[] = "start";
+static char __pyx_k_zeros[] = "zeros";
+static char __pyx_k_format[] = "format";
+static char __pyx_k_import[] = "__import__";
+static char __pyx_k_name_2[] = "__name__";
+static char __pyx_k_struct[] = "struct";
+static char __pyx_k_unpack[] = "unpack";
+static char __pyx_k_xrange[] = "xrange";
+static char __pyx_k_fortran[] = "fortran";
+static char __pyx_k_memview[] = "memview";
+static char __pyx_k_Ellipsis[] = "Ellipsis";
+static char __pyx_k_itemsize[] = "itemsize";
+static char __pyx_k_TypeError[] = "TypeError";
+static char __pyx_k_enumerate[] = "enumerate";
+static char __pyx_k_IndexError[] = "IndexError";
+static char __pyx_k_ValueError[] = "ValueError";
+static char __pyx_k_pyx_vtable[] = "__pyx_vtable__";
+static char __pyx_k_MemoryError[] = "MemoryError";
+static char __pyx_k_RuntimeError[] = "RuntimeError";
+static char __pyx_k_pyx_getbuffer[] = "__pyx_getbuffer";
+static char __pyx_k_allocate_buffer[] = "allocate_buffer";
+static char __pyx_k_dtype_is_object[] = "dtype_is_object";
+static char __pyx_k_strided_and_direct[] = "<strided and direct>";
+static char __pyx_k_strided_and_indirect[] = "<strided and indirect>";
+static char __pyx_k_contiguous_and_direct[] = "<contiguous and direct>";
+static char __pyx_k_MemoryView_of_r_object[] = "<MemoryView of %r object>";
+static char __pyx_k_MemoryView_of_r_at_0x_x[] = "<MemoryView of %r at 0x%x>";
+static char __pyx_k_contiguous_and_indirect[] = "<contiguous and indirect>";
+static char __pyx_k_Cannot_index_with_type_s[] = "Cannot index with type '%s'";
+static char __pyx_k_getbuffer_obj_view_flags[] = "getbuffer(obj, view, flags)";
+static char __pyx_k_Dimension_d_is_not_direct[] = "Dimension %d is not direct";
+static char __pyx_k_Invalid_shape_in_axis_d_d[] = "Invalid shape in axis %d: %d.";
+static char __pyx_k_Index_out_of_bounds_axis_d[] = "Index out of bounds (axis %d)";
+static char __pyx_k_Step_may_not_be_zero_axis_d[] = "Step may not be zero (axis %d)";
+static char __pyx_k_itemsize_0_for_cython_array[] = "itemsize <= 0 for cython.array";
+static char __pyx_k_ndarray_is_not_C_contiguous[] = "ndarray is not C contiguous";
+static char __pyx_k_unable_to_allocate_array_data[] = "unable to allocate array data.";
+static char __pyx_k_strided_and_direct_or_indirect[] = "<strided and direct or indirect>";
+static char __pyx_k_unknown_dtype_code_in_numpy_pxd[] = "unknown dtype code in numpy.pxd (%d)";
+static char __pyx_k_All_dimensions_preceding_dimensi[] = "All dimensions preceding dimension %d must be indexed and not sliced";
+static char __pyx_k_Buffer_view_does_not_expose_stri[] = "Buffer view does not expose strides";
+static char __pyx_k_Can_only_create_a_buffer_that_is[] = "Can only create a buffer that is contiguous in memory.";
+static char __pyx_k_Cannot_transpose_memoryview_with[] = "Cannot transpose memoryview with indirect dimensions";
+static char __pyx_k_Empty_shape_tuple_for_cython_arr[] = "Empty shape tuple for cython.array";
+static char __pyx_k_Format_string_allocated_too_shor[] = "Format string allocated too short, see comment in numpy.pxd";
+static char __pyx_k_Indirect_dimensions_not_supporte[] = "Indirect dimensions not supported";
+static char __pyx_k_Invalid_mode_expected_c_or_fortr[] = "Invalid mode, expected 'c' or 'fortran', got %s";
+static char __pyx_k_Non_native_byte_order_not_suppor[] = "Non-native byte order not supported";
+static char __pyx_k_Out_of_bounds_on_buffer_access_a[] = "Out of bounds on buffer access (axis %d)";
+static char __pyx_k_Unable_to_convert_item_to_object[] = "Unable to convert item to object";
+static char __pyx_k_got_differing_extents_in_dimensi[] = "got differing extents in dimension %d (got %d and %d)";
+static char __pyx_k_ndarray_is_not_Fortran_contiguou[] = "ndarray is not Fortran contiguous";
+static char __pyx_k_unable_to_allocate_shape_and_str[] = "unable to allocate shape and strides.";
+static char __pyx_k_Format_string_allocated_too_shor_2[] = "Format string allocated too short.";
+static PyObject *__pyx_kp_s_Buffer_view_does_not_expose_stri;
+static PyObject *__pyx_kp_s_Can_only_create_a_buffer_that_is;
+static PyObject *__pyx_kp_s_Cannot_index_with_type_s;
+static PyObject *__pyx_n_s_Ellipsis;
+static PyObject *__pyx_kp_s_Empty_shape_tuple_for_cython_arr;
+static PyObject *__pyx_kp_u_Format_string_allocated_too_shor;
+static PyObject *__pyx_kp_u_Format_string_allocated_too_shor_2;
+static PyObject *__pyx_n_s_IndexError;
+static PyObject *__pyx_kp_s_Indirect_dimensions_not_supporte;
+static PyObject *__pyx_kp_s_Invalid_mode_expected_c_or_fortr;
+static PyObject *__pyx_kp_s_Invalid_shape_in_axis_d_d;
+static PyObject *__pyx_n_s_MemoryError;
+static PyObject *__pyx_kp_s_MemoryView_of_r_at_0x_x;
+static PyObject *__pyx_kp_s_MemoryView_of_r_object;
+static PyObject *__pyx_kp_u_Non_native_byte_order_not_suppor;
+static PyObject *__pyx_n_b_O;
+static PyObject *__pyx_kp_s_Out_of_bounds_on_buffer_access_a;
+static PyObject *__pyx_n_s_RuntimeError;
+static PyObject *__pyx_n_s_TypeError;
+static PyObject *__pyx_kp_s_Unable_to_convert_item_to_object;
+static PyObject *__pyx_n_s_ValueError;
+static PyObject *__pyx_n_s_allocate_buffer;
+static PyObject *__pyx_n_s_base;
+static PyObject *__pyx_n_s_c;
+static PyObject *__pyx_n_u_c;
+static PyObject *__pyx_n_s_class;
+static PyObject *__pyx_kp_s_contiguous_and_direct;
+static PyObject *__pyx_kp_s_contiguous_and_indirect;
+static PyObject *__pyx_n_s_copy;
+static PyObject *__pyx_n_s_data;
+static PyObject *__pyx_n_s_dtype;
+static PyObject *__pyx_n_s_dtype_is_object;
+static PyObject *__pyx_n_s_enumerate;
+static PyObject *__pyx_n_s_error;
+static PyObject *__pyx_n_s_f8;
+static PyObject *__pyx_n_s_flags;
+static PyObject *__pyx_n_s_format;
+static PyObject *__pyx_n_s_fortran;
+static PyObject *__pyx_n_u_fortran;
+static PyObject *__pyx_kp_s_got_differing_extents_in_dimensi;
+static PyObject *__pyx_n_s_id;
+static PyObject *__pyx_n_s_import;
+static PyObject *__pyx_n_s_itemsize;
+static PyObject *__pyx_kp_s_itemsize_0_for_cython_array;
+static PyObject *__pyx_n_s_main;
+static PyObject *__pyx_n_s_memview;
+static PyObject *__pyx_n_s_mode;
+static PyObject *__pyx_n_s_name;
+static PyObject *__pyx_n_s_name_2;
+static PyObject *__pyx_kp_u_ndarray_is_not_C_contiguous;
+static PyObject *__pyx_kp_u_ndarray_is_not_Fortran_contiguou;
+static PyObject *__pyx_n_s_ndim;
+static PyObject *__pyx_n_s_numpy;
+static PyObject *__pyx_n_s_obj;
+static PyObject *__pyx_n_s_pack;
+static PyObject *__pyx_n_s_pyx_getbuffer;
+static PyObject *__pyx_n_s_pyx_vtable;
+static PyObject *__pyx_n_s_range;
+static PyObject *__pyx_n_s_shape;
+static PyObject *__pyx_n_s_size;
+static PyObject *__pyx_n_s_start;
+static PyObject *__pyx_n_s_step;
+static PyObject *__pyx_n_s_stop;
+static PyObject *__pyx_kp_s_strided_and_direct;
+static PyObject *__pyx_kp_s_strided_and_direct_or_indirect;
+static PyObject *__pyx_kp_s_strided_and_indirect;
+static PyObject *__pyx_n_s_struct;
+static PyObject *__pyx_n_s_sys;
+static PyObject *__pyx_n_s_test;
+static PyObject *__pyx_n_s_u1;
+static PyObject *__pyx_kp_s_unable_to_allocate_array_data;
+static PyObject *__pyx_kp_s_unable_to_allocate_shape_and_str;
+static PyObject *__pyx_kp_u_unknown_dtype_code_in_numpy_pxd;
+static PyObject *__pyx_n_s_unpack;
+static PyObject *__pyx_n_s_xrange;
+static PyObject *__pyx_n_s_zeros;
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+ */
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+ * memview.dtype_is_object)
+ */
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+
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+ * memview.dtype_is_object)
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+ */
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+
+ /* "View.MemoryView":734
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+ * if isinstance(memview, _memoryviewslice):
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+ * memviewsliceobj.to_object_func,
+ * memviewsliceobj.to_dtype_func,
+ */
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+ __Pyx_GOTREF(__pyx_t_3);
+ if (!(likely(((__pyx_t_3) == Py_None) || likely(__Pyx_TypeTest(__pyx_t_3, __pyx_memoryview_type))))) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 734; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
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+ * return memoryview_fromslice(dst, new_ndim, NULL, NULL, # <<<<<<<<<<<<<<
+ * memview.dtype_is_object)
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+ __Pyx_XDECREF(__pyx_t_3);
+ __Pyx_XDECREF(__pyx_t_9);
+ __Pyx_AddTraceback("View.MemoryView.memview_slice", __pyx_clineno, __pyx_lineno, __pyx_filename);
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+ __pyx_L0:;
+ __Pyx_XDECREF((PyObject *)__pyx_v_memviewsliceobj);
+ __Pyx_XDECREF(__pyx_v_index);
+ __Pyx_XGIVEREF((PyObject *)__pyx_r);
+ __Pyx_RefNannyFinishContext();
+ return __pyx_r;
+}
+
+/* "View.MemoryView":764
+ *
+ * @cname('__pyx_memoryview_slice_memviewslice')
+ * cdef int slice_memviewslice( # <<<<<<<<<<<<<<
+ * __Pyx_memviewslice *dst,
+ * Py_ssize_t shape, Py_ssize_t stride, Py_ssize_t suboffset,
+ */
+
+static int __pyx_memoryview_slice_memviewslice(__Pyx_memviewslice *__pyx_v_dst, Py_ssize_t __pyx_v_shape, Py_ssize_t __pyx_v_stride, Py_ssize_t __pyx_v_suboffset, int __pyx_v_dim, int __pyx_v_new_ndim, int *__pyx_v_suboffset_dim, Py_ssize_t __pyx_v_start, Py_ssize_t __pyx_v_stop, Py_ssize_t __pyx_v_step, int __pyx_v_have_start, int __pyx_v_have_stop, int __pyx_v_have_step, int __pyx_v_is_slice) {
+ Py_ssize_t __pyx_v_new_shape;
+ int __pyx_v_negative_step;
+ int __pyx_r;
+ int __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+
+ /* "View.MemoryView":784
+ * cdef bint negative_step
+ *
+ * if not is_slice: # <<<<<<<<<<<<<<
+ *
+ * if start < 0:
+ */
+ __pyx_t_1 = ((!(__pyx_v_is_slice != 0)) != 0);
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+ *
+ * if start < 0: # <<<<<<<<<<<<<<
+ * start += shape
+ * if not 0 <= start < shape:
+ */
+ __pyx_t_1 = ((__pyx_v_start < 0) != 0);
+ if (__pyx_t_1) {
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+ * if start < 0:
+ * start += shape # <<<<<<<<<<<<<<
+ * if not 0 <= start < shape:
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+ * if not 0 <= start < shape: # <<<<<<<<<<<<<<
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+ * else:
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+
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+ * start += shape
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+ * _err_dim(IndexError, "Index out of bounds (axis %d)", dim) # <<<<<<<<<<<<<<
+ * else:
+ *
+ */
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+ *
+ *
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+ __pyx_t_2 = (__pyx_v_have_start != 0);
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+ * if start < 0:
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+ __pyx_t_2 = ((__pyx_v_start < 0) != 0);
+ if (__pyx_t_2) {
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+ * if start < 0:
+ * start += shape # <<<<<<<<<<<<<<
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+ * start = 0
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+ * if start < 0:
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+ */
+ __pyx_t_2 = ((__pyx_v_start < 0) != 0);
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+ * if negative_step:
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+ }
+ __pyx_L13:;
+ goto __pyx_L12;
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+ * start = 0
+ * elif start >= shape: # <<<<<<<<<<<<<<
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+ __pyx_t_2 = ((__pyx_v_start >= __pyx_v_shape) != 0);
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+ * else:
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+ __pyx_L12:;
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+ __pyx_L11:;
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+ * if stop < 0:
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+ __pyx_t_2 = ((__pyx_v_stop < 0) != 0);
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+ goto __pyx_L7_break;
+ }
+ }
+ __pyx_L7_break:;
+
+ /* "View.MemoryView":1087
+ * break
+ *
+ * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride): # <<<<<<<<<<<<<<
+ * return 'C'
+ * else:
+ */
+ __pyx_t_2 = ((abs_py_ssize_t(__pyx_v_c_stride) <= abs_py_ssize_t(__pyx_v_f_stride)) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1088
+ *
+ * if abs_py_ssize_t(c_stride) <= abs_py_ssize_t(f_stride):
+ * return 'C' # <<<<<<<<<<<<<<
+ * else:
+ * return 'F'
+ */
+ __pyx_r = 'C';
+ goto __pyx_L0;
+ }
+ /*else*/ {
+
+ /* "View.MemoryView":1090
+ * return 'C'
+ * else:
+ * return 'F' # <<<<<<<<<<<<<<
+ *
+ * @cython.cdivision(True)
+ */
+ __pyx_r = 'F';
+ goto __pyx_L0;
+ }
+
+ /* "View.MemoryView":1069
+ *
+ * @cname('__pyx_get_best_slice_order')
+ * cdef char get_best_order(__Pyx_memviewslice *mslice, int ndim) nogil: # <<<<<<<<<<<<<<
+ * """
+ * Figure out the best memory access order for a given slice.
+ */
+
+ /* function exit code */
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "View.MemoryView":1093
+ *
+ * @cython.cdivision(True)
+ * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<<
+ * char *dst_data, Py_ssize_t *dst_strides,
+ * Py_ssize_t *src_shape, Py_ssize_t *dst_shape,
+ */
+
+static void _copy_strided_to_strided(char *__pyx_v_src_data, Py_ssize_t *__pyx_v_src_strides, char *__pyx_v_dst_data, Py_ssize_t *__pyx_v_dst_strides, Py_ssize_t *__pyx_v_src_shape, Py_ssize_t *__pyx_v_dst_shape, int __pyx_v_ndim, size_t __pyx_v_itemsize) {
+ CYTHON_UNUSED Py_ssize_t __pyx_v_i;
+ CYTHON_UNUSED Py_ssize_t __pyx_v_src_extent;
+ Py_ssize_t __pyx_v_dst_extent;
+ Py_ssize_t __pyx_v_src_stride;
+ Py_ssize_t __pyx_v_dst_stride;
+ int __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ Py_ssize_t __pyx_t_4;
+ Py_ssize_t __pyx_t_5;
+
+ /* "View.MemoryView":1100
+ *
+ * cdef Py_ssize_t i
+ * cdef Py_ssize_t src_extent = src_shape[0] # <<<<<<<<<<<<<<
+ * cdef Py_ssize_t dst_extent = dst_shape[0]
+ * cdef Py_ssize_t src_stride = src_strides[0]
+ */
+ __pyx_v_src_extent = (__pyx_v_src_shape[0]);
+
+ /* "View.MemoryView":1101
+ * cdef Py_ssize_t i
+ * cdef Py_ssize_t src_extent = src_shape[0]
+ * cdef Py_ssize_t dst_extent = dst_shape[0] # <<<<<<<<<<<<<<
+ * cdef Py_ssize_t src_stride = src_strides[0]
+ * cdef Py_ssize_t dst_stride = dst_strides[0]
+ */
+ __pyx_v_dst_extent = (__pyx_v_dst_shape[0]);
+
+ /* "View.MemoryView":1102
+ * cdef Py_ssize_t src_extent = src_shape[0]
+ * cdef Py_ssize_t dst_extent = dst_shape[0]
+ * cdef Py_ssize_t src_stride = src_strides[0] # <<<<<<<<<<<<<<
+ * cdef Py_ssize_t dst_stride = dst_strides[0]
+ *
+ */
+ __pyx_v_src_stride = (__pyx_v_src_strides[0]);
+
+ /* "View.MemoryView":1103
+ * cdef Py_ssize_t dst_extent = dst_shape[0]
+ * cdef Py_ssize_t src_stride = src_strides[0]
+ * cdef Py_ssize_t dst_stride = dst_strides[0] # <<<<<<<<<<<<<<
+ *
+ * if ndim == 1:
+ */
+ __pyx_v_dst_stride = (__pyx_v_dst_strides[0]);
+
+ /* "View.MemoryView":1105
+ * cdef Py_ssize_t dst_stride = dst_strides[0]
+ *
+ * if ndim == 1: # <<<<<<<<<<<<<<
+ * if (src_stride > 0 and dst_stride > 0 and
+ * <size_t> src_stride == itemsize == <size_t> dst_stride):
+ */
+ __pyx_t_1 = ((__pyx_v_ndim == 1) != 0);
+ if (__pyx_t_1) {
+
+ /* "View.MemoryView":1106
+ *
+ * if ndim == 1:
+ * if (src_stride > 0 and dst_stride > 0 and # <<<<<<<<<<<<<<
+ * <size_t> src_stride == itemsize == <size_t> dst_stride):
+ * memcpy(dst_data, src_data, itemsize * dst_extent)
+ */
+ __pyx_t_2 = ((__pyx_v_src_stride > 0) != 0);
+ if (__pyx_t_2) {
+ } else {
+ __pyx_t_1 = __pyx_t_2;
+ goto __pyx_L5_bool_binop_done;
+ }
+ __pyx_t_2 = ((__pyx_v_dst_stride > 0) != 0);
+ if (__pyx_t_2) {
+ } else {
+ __pyx_t_1 = __pyx_t_2;
+ goto __pyx_L5_bool_binop_done;
+ }
+
+ /* "View.MemoryView":1107
+ * if ndim == 1:
+ * if (src_stride > 0 and dst_stride > 0 and
+ * <size_t> src_stride == itemsize == <size_t> dst_stride): # <<<<<<<<<<<<<<
+ * memcpy(dst_data, src_data, itemsize * dst_extent)
+ * else:
+ */
+ __pyx_t_2 = (((size_t)__pyx_v_src_stride) == __pyx_v_itemsize);
+ if (__pyx_t_2) {
+ __pyx_t_2 = (__pyx_v_itemsize == ((size_t)__pyx_v_dst_stride));
+ }
+ __pyx_t_3 = (__pyx_t_2 != 0);
+ __pyx_t_1 = __pyx_t_3;
+ __pyx_L5_bool_binop_done:;
+ if (__pyx_t_1) {
+
+ /* "View.MemoryView":1108
+ * if (src_stride > 0 and dst_stride > 0 and
+ * <size_t> src_stride == itemsize == <size_t> dst_stride):
+ * memcpy(dst_data, src_data, itemsize * dst_extent) # <<<<<<<<<<<<<<
+ * else:
+ * for i in range(dst_extent):
+ */
+ memcpy(__pyx_v_dst_data, __pyx_v_src_data, (__pyx_v_itemsize * __pyx_v_dst_extent));
+ goto __pyx_L4;
+ }
+ /*else*/ {
+
+ /* "View.MemoryView":1110
+ * memcpy(dst_data, src_data, itemsize * dst_extent)
+ * else:
+ * for i in range(dst_extent): # <<<<<<<<<<<<<<
+ * memcpy(dst_data, src_data, itemsize)
+ * src_data += src_stride
+ */
+ __pyx_t_4 = __pyx_v_dst_extent;
+ for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
+ __pyx_v_i = __pyx_t_5;
+
+ /* "View.MemoryView":1111
+ * else:
+ * for i in range(dst_extent):
+ * memcpy(dst_data, src_data, itemsize) # <<<<<<<<<<<<<<
+ * src_data += src_stride
+ * dst_data += dst_stride
+ */
+ memcpy(__pyx_v_dst_data, __pyx_v_src_data, __pyx_v_itemsize);
+
+ /* "View.MemoryView":1112
+ * for i in range(dst_extent):
+ * memcpy(dst_data, src_data, itemsize)
+ * src_data += src_stride # <<<<<<<<<<<<<<
+ * dst_data += dst_stride
+ * else:
+ */
+ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride);
+
+ /* "View.MemoryView":1113
+ * memcpy(dst_data, src_data, itemsize)
+ * src_data += src_stride
+ * dst_data += dst_stride # <<<<<<<<<<<<<<
+ * else:
+ * for i in range(dst_extent):
+ */
+ __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride);
+ }
+ }
+ __pyx_L4:;
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "View.MemoryView":1115
+ * dst_data += dst_stride
+ * else:
+ * for i in range(dst_extent): # <<<<<<<<<<<<<<
+ * _copy_strided_to_strided(src_data, src_strides + 1,
+ * dst_data, dst_strides + 1,
+ */
+ __pyx_t_4 = __pyx_v_dst_extent;
+ for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_4; __pyx_t_5+=1) {
+ __pyx_v_i = __pyx_t_5;
+
+ /* "View.MemoryView":1116
+ * else:
+ * for i in range(dst_extent):
+ * _copy_strided_to_strided(src_data, src_strides + 1, # <<<<<<<<<<<<<<
+ * dst_data, dst_strides + 1,
+ * src_shape + 1, dst_shape + 1,
+ */
+ _copy_strided_to_strided(__pyx_v_src_data, (__pyx_v_src_strides + 1), __pyx_v_dst_data, (__pyx_v_dst_strides + 1), (__pyx_v_src_shape + 1), (__pyx_v_dst_shape + 1), (__pyx_v_ndim - 1), __pyx_v_itemsize);
+
+ /* "View.MemoryView":1120
+ * src_shape + 1, dst_shape + 1,
+ * ndim - 1, itemsize)
+ * src_data += src_stride # <<<<<<<<<<<<<<
+ * dst_data += dst_stride
+ *
+ */
+ __pyx_v_src_data = (__pyx_v_src_data + __pyx_v_src_stride);
+
+ /* "View.MemoryView":1121
+ * ndim - 1, itemsize)
+ * src_data += src_stride
+ * dst_data += dst_stride # <<<<<<<<<<<<<<
+ *
+ * cdef void copy_strided_to_strided(__Pyx_memviewslice *src,
+ */
+ __pyx_v_dst_data = (__pyx_v_dst_data + __pyx_v_dst_stride);
+ }
+ }
+ __pyx_L3:;
+
+ /* "View.MemoryView":1093
+ *
+ * @cython.cdivision(True)
+ * cdef void _copy_strided_to_strided(char *src_data, Py_ssize_t *src_strides, # <<<<<<<<<<<<<<
+ * char *dst_data, Py_ssize_t *dst_strides,
+ * Py_ssize_t *src_shape, Py_ssize_t *dst_shape,
+ */
+
+ /* function exit code */
+}
+
+/* "View.MemoryView":1123
+ * dst_data += dst_stride
+ *
+ * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<<
+ * __Pyx_memviewslice *dst,
+ * int ndim, size_t itemsize) nogil:
+ */
+
+static void copy_strided_to_strided(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_dst, int __pyx_v_ndim, size_t __pyx_v_itemsize) {
+
+ /* "View.MemoryView":1126
+ * __Pyx_memviewslice *dst,
+ * int ndim, size_t itemsize) nogil:
+ * _copy_strided_to_strided(src.data, src.strides, dst.data, dst.strides, # <<<<<<<<<<<<<<
+ * src.shape, dst.shape, ndim, itemsize)
+ *
+ */
+ _copy_strided_to_strided(__pyx_v_src->data, __pyx_v_src->strides, __pyx_v_dst->data, __pyx_v_dst->strides, __pyx_v_src->shape, __pyx_v_dst->shape, __pyx_v_ndim, __pyx_v_itemsize);
+
+ /* "View.MemoryView":1123
+ * dst_data += dst_stride
+ *
+ * cdef void copy_strided_to_strided(__Pyx_memviewslice *src, # <<<<<<<<<<<<<<
+ * __Pyx_memviewslice *dst,
+ * int ndim, size_t itemsize) nogil:
+ */
+
+ /* function exit code */
+}
+
+/* "View.MemoryView":1130
+ *
+ * @cname('__pyx_memoryview_slice_get_size')
+ * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<<
+ * "Return the size of the memory occupied by the slice in number of bytes"
+ * cdef int i
+ */
+
+static Py_ssize_t __pyx_memoryview_slice_get_size(__Pyx_memviewslice *__pyx_v_src, int __pyx_v_ndim) {
+ int __pyx_v_i;
+ Py_ssize_t __pyx_v_size;
+ Py_ssize_t __pyx_r;
+ Py_ssize_t __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+
+ /* "View.MemoryView":1133
+ * "Return the size of the memory occupied by the slice in number of bytes"
+ * cdef int i
+ * cdef Py_ssize_t size = src.memview.view.itemsize # <<<<<<<<<<<<<<
+ *
+ * for i in range(ndim):
+ */
+ __pyx_t_1 = __pyx_v_src->memview->view.itemsize;
+ __pyx_v_size = __pyx_t_1;
+
+ /* "View.MemoryView":1135
+ * cdef Py_ssize_t size = src.memview.view.itemsize
+ *
+ * for i in range(ndim): # <<<<<<<<<<<<<<
+ * size *= src.shape[i]
+ *
+ */
+ __pyx_t_2 = __pyx_v_ndim;
+ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
+ __pyx_v_i = __pyx_t_3;
+
+ /* "View.MemoryView":1136
+ *
+ * for i in range(ndim):
+ * size *= src.shape[i] # <<<<<<<<<<<<<<
+ *
+ * return size
+ */
+ __pyx_v_size = (__pyx_v_size * (__pyx_v_src->shape[__pyx_v_i]));
+ }
+
+ /* "View.MemoryView":1138
+ * size *= src.shape[i]
+ *
+ * return size # <<<<<<<<<<<<<<
+ *
+ * @cname('__pyx_fill_contig_strides_array')
+ */
+ __pyx_r = __pyx_v_size;
+ goto __pyx_L0;
+
+ /* "View.MemoryView":1130
+ *
+ * @cname('__pyx_memoryview_slice_get_size')
+ * cdef Py_ssize_t slice_get_size(__Pyx_memviewslice *src, int ndim) nogil: # <<<<<<<<<<<<<<
+ * "Return the size of the memory occupied by the slice in number of bytes"
+ * cdef int i
+ */
+
+ /* function exit code */
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "View.MemoryView":1141
+ *
+ * @cname('__pyx_fill_contig_strides_array')
+ * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<<
+ * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride,
+ * int ndim, char order) nogil:
+ */
+
+static Py_ssize_t __pyx_fill_contig_strides_array(Py_ssize_t *__pyx_v_shape, Py_ssize_t *__pyx_v_strides, Py_ssize_t __pyx_v_stride, int __pyx_v_ndim, char __pyx_v_order) {
+ int __pyx_v_idx;
+ Py_ssize_t __pyx_r;
+ int __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+
+ /* "View.MemoryView":1150
+ * cdef int idx
+ *
+ * if order == 'F': # <<<<<<<<<<<<<<
+ * for idx in range(ndim):
+ * strides[idx] = stride
+ */
+ __pyx_t_1 = ((__pyx_v_order == 'F') != 0);
+ if (__pyx_t_1) {
+
+ /* "View.MemoryView":1151
+ *
+ * if order == 'F':
+ * for idx in range(ndim): # <<<<<<<<<<<<<<
+ * strides[idx] = stride
+ * stride = stride * shape[idx]
+ */
+ __pyx_t_2 = __pyx_v_ndim;
+ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_2; __pyx_t_3+=1) {
+ __pyx_v_idx = __pyx_t_3;
+
+ /* "View.MemoryView":1152
+ * if order == 'F':
+ * for idx in range(ndim):
+ * strides[idx] = stride # <<<<<<<<<<<<<<
+ * stride = stride * shape[idx]
+ * else:
+ */
+ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride;
+
+ /* "View.MemoryView":1153
+ * for idx in range(ndim):
+ * strides[idx] = stride
+ * stride = stride * shape[idx] # <<<<<<<<<<<<<<
+ * else:
+ * for idx in range(ndim - 1, -1, -1):
+ */
+ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx]));
+ }
+ goto __pyx_L3;
+ }
+ /*else*/ {
+
+ /* "View.MemoryView":1155
+ * stride = stride * shape[idx]
+ * else:
+ * for idx in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<<
+ * strides[idx] = stride
+ * stride = stride * shape[idx]
+ */
+ for (__pyx_t_2 = (__pyx_v_ndim - 1); __pyx_t_2 > -1; __pyx_t_2-=1) {
+ __pyx_v_idx = __pyx_t_2;
+
+ /* "View.MemoryView":1156
+ * else:
+ * for idx in range(ndim - 1, -1, -1):
+ * strides[idx] = stride # <<<<<<<<<<<<<<
+ * stride = stride * shape[idx]
+ *
+ */
+ (__pyx_v_strides[__pyx_v_idx]) = __pyx_v_stride;
+
+ /* "View.MemoryView":1157
+ * for idx in range(ndim - 1, -1, -1):
+ * strides[idx] = stride
+ * stride = stride * shape[idx] # <<<<<<<<<<<<<<
+ *
+ * return stride
+ */
+ __pyx_v_stride = (__pyx_v_stride * (__pyx_v_shape[__pyx_v_idx]));
+ }
+ }
+ __pyx_L3:;
+
+ /* "View.MemoryView":1159
+ * stride = stride * shape[idx]
+ *
+ * return stride # <<<<<<<<<<<<<<
+ *
+ * @cname('__pyx_memoryview_copy_data_to_temp')
+ */
+ __pyx_r = __pyx_v_stride;
+ goto __pyx_L0;
+
+ /* "View.MemoryView":1141
+ *
+ * @cname('__pyx_fill_contig_strides_array')
+ * cdef Py_ssize_t fill_contig_strides_array( # <<<<<<<<<<<<<<
+ * Py_ssize_t *shape, Py_ssize_t *strides, Py_ssize_t stride,
+ * int ndim, char order) nogil:
+ */
+
+ /* function exit code */
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "View.MemoryView":1162
+ *
+ * @cname('__pyx_memoryview_copy_data_to_temp')
+ * cdef void *copy_data_to_temp(__Pyx_memviewslice *src, # <<<<<<<<<<<<<<
+ * __Pyx_memviewslice *tmpslice,
+ * char order,
+ */
+
+static void *__pyx_memoryview_copy_data_to_temp(__Pyx_memviewslice *__pyx_v_src, __Pyx_memviewslice *__pyx_v_tmpslice, char __pyx_v_order, int __pyx_v_ndim) {
+ int __pyx_v_i;
+ void *__pyx_v_result;
+ size_t __pyx_v_itemsize;
+ size_t __pyx_v_size;
+ void *__pyx_r;
+ Py_ssize_t __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ struct __pyx_memoryview_obj *__pyx_t_4;
+ int __pyx_t_5;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+
+ /* "View.MemoryView":1173
+ * cdef void *result
+ *
+ * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<<
+ * cdef size_t size = slice_get_size(src, ndim)
+ *
+ */
+ __pyx_t_1 = __pyx_v_src->memview->view.itemsize;
+ __pyx_v_itemsize = __pyx_t_1;
+
+ /* "View.MemoryView":1174
+ *
+ * cdef size_t itemsize = src.memview.view.itemsize
+ * cdef size_t size = slice_get_size(src, ndim) # <<<<<<<<<<<<<<
+ *
+ * result = malloc(size)
+ */
+ __pyx_v_size = __pyx_memoryview_slice_get_size(__pyx_v_src, __pyx_v_ndim);
+
+ /* "View.MemoryView":1176
+ * cdef size_t size = slice_get_size(src, ndim)
+ *
+ * result = malloc(size) # <<<<<<<<<<<<<<
+ * if not result:
+ * _err(MemoryError, NULL)
+ */
+ __pyx_v_result = malloc(__pyx_v_size);
+
+ /* "View.MemoryView":1177
+ *
+ * result = malloc(size)
+ * if not result: # <<<<<<<<<<<<<<
+ * _err(MemoryError, NULL)
+ *
+ */
+ __pyx_t_2 = ((!(__pyx_v_result != 0)) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1178
+ * result = malloc(size)
+ * if not result:
+ * _err(MemoryError, NULL) # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_t_3 = __pyx_memoryview_err(__pyx_builtin_MemoryError, NULL); if (unlikely(__pyx_t_3 == -1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 1178; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "View.MemoryView":1181
+ *
+ *
+ * tmpslice.data = <char *> result # <<<<<<<<<<<<<<
+ * tmpslice.memview = src.memview
+ * for i in range(ndim):
+ */
+ __pyx_v_tmpslice->data = ((char *)__pyx_v_result);
+
+ /* "View.MemoryView":1182
+ *
+ * tmpslice.data = <char *> result
+ * tmpslice.memview = src.memview # <<<<<<<<<<<<<<
+ * for i in range(ndim):
+ * tmpslice.shape[i] = src.shape[i]
+ */
+ __pyx_t_4 = __pyx_v_src->memview;
+ __pyx_v_tmpslice->memview = __pyx_t_4;
+
+ /* "View.MemoryView":1183
+ * tmpslice.data = <char *> result
+ * tmpslice.memview = src.memview
+ * for i in range(ndim): # <<<<<<<<<<<<<<
+ * tmpslice.shape[i] = src.shape[i]
+ * tmpslice.suboffsets[i] = -1
+ */
+ __pyx_t_3 = __pyx_v_ndim;
+ for (__pyx_t_5 = 0; __pyx_t_5 < __pyx_t_3; __pyx_t_5+=1) {
+ __pyx_v_i = __pyx_t_5;
+
+ /* "View.MemoryView":1184
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+
+static int __pyx_memoryview_copy_contents(__Pyx_memviewslice __pyx_v_src, __Pyx_memviewslice __pyx_v_dst, int __pyx_v_src_ndim, int __pyx_v_dst_ndim, int __pyx_v_dtype_is_object) {
+ void *__pyx_v_tmpdata;
+ size_t __pyx_v_itemsize;
+ int __pyx_v_i;
+ char __pyx_v_order;
+ int __pyx_v_broadcasting;
+ int __pyx_v_direct_copy;
+ __Pyx_memviewslice __pyx_v_tmp;
+ int __pyx_v_ndim;
+ int __pyx_r;
+ Py_ssize_t __pyx_t_1;
+ int __pyx_t_2;
+ int __pyx_t_3;
+ int __pyx_t_4;
+ int __pyx_t_5;
+ void *__pyx_t_6;
+ int __pyx_t_7;
+ int __pyx_lineno = 0;
+ const char *__pyx_filename = NULL;
+ int __pyx_clineno = 0;
+
+ /* "View.MemoryView":1230
+ * Check for overlapping memory and verify the shapes.
+ * """
+ * cdef void *tmpdata = NULL # <<<<<<<<<<<<<<
+ * cdef size_t itemsize = src.memview.view.itemsize
+ * cdef int i
+ */
+ __pyx_v_tmpdata = NULL;
+
+ /* "View.MemoryView":1231
+ * """
+ * cdef void *tmpdata = NULL
+ * cdef size_t itemsize = src.memview.view.itemsize # <<<<<<<<<<<<<<
+ * cdef int i
+ * cdef char order = get_best_order(&src, src_ndim)
+ */
+ __pyx_t_1 = __pyx_v_src.memview->view.itemsize;
+ __pyx_v_itemsize = __pyx_t_1;
+
+ /* "View.MemoryView":1233
+ * cdef size_t itemsize = src.memview.view.itemsize
+ * cdef int i
+ * cdef char order = get_best_order(&src, src_ndim) # <<<<<<<<<<<<<<
+ * cdef bint broadcasting = False
+ * cdef bint direct_copy = False
+ */
+ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_src), __pyx_v_src_ndim);
+
+ /* "View.MemoryView":1234
+ * cdef int i
+ * cdef char order = get_best_order(&src, src_ndim)
+ * cdef bint broadcasting = False # <<<<<<<<<<<<<<
+ * cdef bint direct_copy = False
+ * cdef __Pyx_memviewslice tmp
+ */
+ __pyx_v_broadcasting = 0;
+
+ /* "View.MemoryView":1235
+ * cdef char order = get_best_order(&src, src_ndim)
+ * cdef bint broadcasting = False
+ * cdef bint direct_copy = False # <<<<<<<<<<<<<<
+ * cdef __Pyx_memviewslice tmp
+ *
+ */
+ __pyx_v_direct_copy = 0;
+
+ /* "View.MemoryView":1238
+ * cdef __Pyx_memviewslice tmp
+ *
+ * if src_ndim < dst_ndim: # <<<<<<<<<<<<<<
+ * broadcast_leading(&src, src_ndim, dst_ndim)
+ * elif dst_ndim < src_ndim:
+ */
+ __pyx_t_2 = ((__pyx_v_src_ndim < __pyx_v_dst_ndim) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1239
+ *
+ * if src_ndim < dst_ndim:
+ * broadcast_leading(&src, src_ndim, dst_ndim) # <<<<<<<<<<<<<<
+ * elif dst_ndim < src_ndim:
+ * broadcast_leading(&dst, dst_ndim, src_ndim)
+ */
+ __pyx_memoryview_broadcast_leading((&__pyx_v_src), __pyx_v_src_ndim, __pyx_v_dst_ndim);
+ goto __pyx_L3;
+ }
+
+ /* "View.MemoryView":1240
+ * if src_ndim < dst_ndim:
+ * broadcast_leading(&src, src_ndim, dst_ndim)
+ * elif dst_ndim < src_ndim: # <<<<<<<<<<<<<<
+ * broadcast_leading(&dst, dst_ndim, src_ndim)
+ *
+ */
+ __pyx_t_2 = ((__pyx_v_dst_ndim < __pyx_v_src_ndim) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1241
+ * broadcast_leading(&src, src_ndim, dst_ndim)
+ * elif dst_ndim < src_ndim:
+ * broadcast_leading(&dst, dst_ndim, src_ndim) # <<<<<<<<<<<<<<
+ *
+ * cdef int ndim = max(src_ndim, dst_ndim)
+ */
+ __pyx_memoryview_broadcast_leading((&__pyx_v_dst), __pyx_v_dst_ndim, __pyx_v_src_ndim);
+ goto __pyx_L3;
+ }
+ __pyx_L3:;
+
+ /* "View.MemoryView":1243
+ * broadcast_leading(&dst, dst_ndim, src_ndim)
+ *
+ * cdef int ndim = max(src_ndim, dst_ndim) # <<<<<<<<<<<<<<
+ *
+ * for i in range(ndim):
+ */
+ __pyx_t_3 = __pyx_v_dst_ndim;
+ __pyx_t_4 = __pyx_v_src_ndim;
+ if (((__pyx_t_3 > __pyx_t_4) != 0)) {
+ __pyx_t_5 = __pyx_t_3;
+ } else {
+ __pyx_t_5 = __pyx_t_4;
+ }
+ __pyx_v_ndim = __pyx_t_5;
+
+ /* "View.MemoryView":1245
+ * cdef int ndim = max(src_ndim, dst_ndim)
+ *
+ * for i in range(ndim): # <<<<<<<<<<<<<<
+ * if src.shape[i] != dst.shape[i]:
+ * if src.shape[i] == 1:
+ */
+ __pyx_t_5 = __pyx_v_ndim;
+ for (__pyx_t_3 = 0; __pyx_t_3 < __pyx_t_5; __pyx_t_3+=1) {
+ __pyx_v_i = __pyx_t_3;
+
+ /* "View.MemoryView":1246
+ *
+ * for i in range(ndim):
+ * if src.shape[i] != dst.shape[i]: # <<<<<<<<<<<<<<
+ * if src.shape[i] == 1:
+ * broadcasting = True
+ */
+ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) != (__pyx_v_dst.shape[__pyx_v_i])) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1247
+ * for i in range(ndim):
+ * if src.shape[i] != dst.shape[i]:
+ * if src.shape[i] == 1: # <<<<<<<<<<<<<<
+ * broadcasting = True
+ * src.strides[i] = 0
+ */
+ __pyx_t_2 = (((__pyx_v_src.shape[__pyx_v_i]) == 1) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1248
+ * if src.shape[i] != dst.shape[i]:
+ * if src.shape[i] == 1:
+ * broadcasting = True # <<<<<<<<<<<<<<
+ * src.strides[i] = 0
+ * else:
+ */
+ __pyx_v_broadcasting = 1;
+
+ /* "View.MemoryView":1249
+ * if src.shape[i] == 1:
+ * broadcasting = True
+ * src.strides[i] = 0 # <<<<<<<<<<<<<<
+ * else:
+ * _err_extents(i, dst.shape[i], src.shape[i])
+ */
+ (__pyx_v_src.strides[__pyx_v_i]) = 0;
+ goto __pyx_L7;
+ }
+ /*else*/ {
+
+ /* "View.MemoryView":1251
+ * src.strides[i] = 0
+ * else:
+ * _err_extents(i, dst.shape[i], src.shape[i]) # <<<<<<<<<<<<<<
+ *
+ * if src.suboffsets[i] >= 0:
+ */
+ __pyx_t_4 = __pyx_memoryview_err_extents(__pyx_v_i, (__pyx_v_dst.shape[__pyx_v_i]), (__pyx_v_src.shape[__pyx_v_i])); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 1251; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ }
+ __pyx_L7:;
+ goto __pyx_L6;
+ }
+ __pyx_L6:;
+
+ /* "View.MemoryView":1253
+ * _err_extents(i, dst.shape[i], src.shape[i])
+ *
+ * if src.suboffsets[i] >= 0: # <<<<<<<<<<<<<<
+ * _err_dim(ValueError, "Dimension %d is not direct", i)
+ *
+ */
+ __pyx_t_2 = (((__pyx_v_src.suboffsets[__pyx_v_i]) >= 0) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1254
+ *
+ * if src.suboffsets[i] >= 0:
+ * _err_dim(ValueError, "Dimension %d is not direct", i) # <<<<<<<<<<<<<<
+ *
+ * if slices_overlap(&src, &dst, ndim, itemsize):
+ */
+ __pyx_t_4 = __pyx_memoryview_err_dim(__pyx_builtin_ValueError, __pyx_k_Dimension_d_is_not_direct, __pyx_v_i); if (unlikely(__pyx_t_4 == -1)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 1254; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L8;
+ }
+ __pyx_L8:;
+ }
+
+ /* "View.MemoryView":1256
+ * _err_dim(ValueError, "Dimension %d is not direct", i)
+ *
+ * if slices_overlap(&src, &dst, ndim, itemsize): # <<<<<<<<<<<<<<
+ *
+ * if not slice_is_contig(&src, order, ndim):
+ */
+ __pyx_t_2 = (__pyx_slices_overlap((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1258
+ * if slices_overlap(&src, &dst, ndim, itemsize):
+ *
+ * if not slice_is_contig(&src, order, ndim): # <<<<<<<<<<<<<<
+ * order = get_best_order(&dst, ndim)
+ *
+ */
+ __pyx_t_2 = ((!(__pyx_memviewslice_is_contig((&__pyx_v_src), __pyx_v_order, __pyx_v_ndim) != 0)) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1259
+ *
+ * if not slice_is_contig(&src, order, ndim):
+ * order = get_best_order(&dst, ndim) # <<<<<<<<<<<<<<
+ *
+ * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim)
+ */
+ __pyx_v_order = __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim);
+ goto __pyx_L10;
+ }
+ __pyx_L10:;
+
+ /* "View.MemoryView":1261
+ * order = get_best_order(&dst, ndim)
+ *
+ * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim) # <<<<<<<<<<<<<<
+ * src = tmp
+ *
+ */
+ __pyx_t_6 = __pyx_memoryview_copy_data_to_temp((&__pyx_v_src), (&__pyx_v_tmp), __pyx_v_order, __pyx_v_ndim); if (unlikely(__pyx_t_6 == NULL)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 1261; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ __pyx_v_tmpdata = __pyx_t_6;
+
+ /* "View.MemoryView":1262
+ *
+ * tmpdata = copy_data_to_temp(&src, &tmp, order, ndim)
+ * src = tmp # <<<<<<<<<<<<<<
+ *
+ * if not broadcasting:
+ */
+ __pyx_v_src = __pyx_v_tmp;
+ goto __pyx_L9;
+ }
+ __pyx_L9:;
+
+ /* "View.MemoryView":1264
+ * src = tmp
+ *
+ * if not broadcasting: # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_t_2 = ((!(__pyx_v_broadcasting != 0)) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1267
+ *
+ *
+ * if slice_is_contig(&src, 'C', ndim): # <<<<<<<<<<<<<<
+ * direct_copy = slice_is_contig(&dst, 'C', ndim)
+ * elif slice_is_contig(&src, 'F', ndim):
+ */
+ __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'C', __pyx_v_ndim) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1268
+ *
+ * if slice_is_contig(&src, 'C', ndim):
+ * direct_copy = slice_is_contig(&dst, 'C', ndim) # <<<<<<<<<<<<<<
+ * elif slice_is_contig(&src, 'F', ndim):
+ * direct_copy = slice_is_contig(&dst, 'F', ndim)
+ */
+ __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'C', __pyx_v_ndim);
+ goto __pyx_L12;
+ }
+
+ /* "View.MemoryView":1269
+ * if slice_is_contig(&src, 'C', ndim):
+ * direct_copy = slice_is_contig(&dst, 'C', ndim)
+ * elif slice_is_contig(&src, 'F', ndim): # <<<<<<<<<<<<<<
+ * direct_copy = slice_is_contig(&dst, 'F', ndim)
+ *
+ */
+ __pyx_t_2 = (__pyx_memviewslice_is_contig((&__pyx_v_src), 'F', __pyx_v_ndim) != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1270
+ * direct_copy = slice_is_contig(&dst, 'C', ndim)
+ * elif slice_is_contig(&src, 'F', ndim):
+ * direct_copy = slice_is_contig(&dst, 'F', ndim) # <<<<<<<<<<<<<<
+ *
+ * if direct_copy:
+ */
+ __pyx_v_direct_copy = __pyx_memviewslice_is_contig((&__pyx_v_dst), 'F', __pyx_v_ndim);
+ goto __pyx_L12;
+ }
+ __pyx_L12:;
+
+ /* "View.MemoryView":1272
+ * direct_copy = slice_is_contig(&dst, 'F', ndim)
+ *
+ * if direct_copy: # <<<<<<<<<<<<<<
+ *
+ * refcount_copying(&dst, dtype_is_object, ndim, False)
+ */
+ __pyx_t_2 = (__pyx_v_direct_copy != 0);
+ if (__pyx_t_2) {
+
+ /* "View.MemoryView":1274
+ * if direct_copy:
+ *
+ * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<<
+ * memcpy(dst.data, src.data, slice_get_size(&src, ndim))
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ */
+ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0);
+
+ /* "View.MemoryView":1275
+ *
+ * refcount_copying(&dst, dtype_is_object, ndim, False)
+ * memcpy(dst.data, src.data, slice_get_size(&src, ndim)) # <<<<<<<<<<<<<<
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ * free(tmpdata)
+ */
+ memcpy(__pyx_v_dst.data, __pyx_v_src.data, __pyx_memoryview_slice_get_size((&__pyx_v_src), __pyx_v_ndim));
+
+ /* "View.MemoryView":1276
+ * refcount_copying(&dst, dtype_is_object, ndim, False)
+ * memcpy(dst.data, src.data, slice_get_size(&src, ndim))
+ * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<<
+ * free(tmpdata)
+ * return 0
+ */
+ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1);
+
+ /* "View.MemoryView":1277
+ * memcpy(dst.data, src.data, slice_get_size(&src, ndim))
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ * free(tmpdata) # <<<<<<<<<<<<<<
+ * return 0
+ *
+ */
+ free(__pyx_v_tmpdata);
+
+ /* "View.MemoryView":1278
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ * free(tmpdata)
+ * return 0 # <<<<<<<<<<<<<<
+ *
+ * if order == 'F' == get_best_order(&dst, ndim):
+ */
+ __pyx_r = 0;
+ goto __pyx_L0;
+ }
+ goto __pyx_L11;
+ }
+ __pyx_L11:;
+
+ /* "View.MemoryView":1280
+ * return 0
+ *
+ * if order == 'F' == get_best_order(&dst, ndim): # <<<<<<<<<<<<<<
+ *
+ *
+ */
+ __pyx_t_2 = (__pyx_v_order == 'F');
+ if (__pyx_t_2) {
+ __pyx_t_2 = ('F' == __pyx_get_best_slice_order((&__pyx_v_dst), __pyx_v_ndim));
+ }
+ __pyx_t_7 = (__pyx_t_2 != 0);
+ if (__pyx_t_7) {
+
+ /* "View.MemoryView":1283
+ *
+ *
+ * transpose_memslice(&src) # <<<<<<<<<<<<<<
+ * transpose_memslice(&dst)
+ *
+ */
+ __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_src)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 1283; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+
+ /* "View.MemoryView":1284
+ *
+ * transpose_memslice(&src)
+ * transpose_memslice(&dst) # <<<<<<<<<<<<<<
+ *
+ * refcount_copying(&dst, dtype_is_object, ndim, False)
+ */
+ __pyx_t_5 = __pyx_memslice_transpose((&__pyx_v_dst)); if (unlikely(__pyx_t_5 == 0)) {__pyx_filename = __pyx_f[3]; __pyx_lineno = 1284; __pyx_clineno = __LINE__; goto __pyx_L1_error;}
+ goto __pyx_L14;
+ }
+ __pyx_L14:;
+
+ /* "View.MemoryView":1286
+ * transpose_memslice(&dst)
+ *
+ * refcount_copying(&dst, dtype_is_object, ndim, False) # <<<<<<<<<<<<<<
+ * copy_strided_to_strided(&src, &dst, ndim, itemsize)
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ */
+ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 0);
+
+ /* "View.MemoryView":1287
+ *
+ * refcount_copying(&dst, dtype_is_object, ndim, False)
+ * copy_strided_to_strided(&src, &dst, ndim, itemsize) # <<<<<<<<<<<<<<
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ *
+ */
+ copy_strided_to_strided((&__pyx_v_src), (&__pyx_v_dst), __pyx_v_ndim, __pyx_v_itemsize);
+
+ /* "View.MemoryView":1288
+ * refcount_copying(&dst, dtype_is_object, ndim, False)
+ * copy_strided_to_strided(&src, &dst, ndim, itemsize)
+ * refcount_copying(&dst, dtype_is_object, ndim, True) # <<<<<<<<<<<<<<
+ *
+ * free(tmpdata)
+ */
+ __pyx_memoryview_refcount_copying((&__pyx_v_dst), __pyx_v_dtype_is_object, __pyx_v_ndim, 1);
+
+ /* "View.MemoryView":1290
+ * refcount_copying(&dst, dtype_is_object, ndim, True)
+ *
+ * free(tmpdata) # <<<<<<<<<<<<<<
+ * return 0
+ *
+ */
+ free(__pyx_v_tmpdata);
+
+ /* "View.MemoryView":1291
+ *
+ * free(tmpdata)
+ * return 0 # <<<<<<<<<<<<<<
+ *
+ * @cname('__pyx_memoryview_broadcast_leading')
+ */
+ __pyx_r = 0;
+ goto __pyx_L0;
+
+ /* "View.MemoryView":1222
+ *
+ * @cname('__pyx_memoryview_copy_contents')
+ * cdef int memoryview_copy_contents(__Pyx_memviewslice src, # <<<<<<<<<<<<<<
+ * __Pyx_memviewslice dst,
+ * int src_ndim, int dst_ndim,
+ */
+
+ /* function exit code */
+ __pyx_L1_error:;
+ {
+ #ifdef WITH_THREAD
+ PyGILState_STATE __pyx_gilstate_save = PyGILState_Ensure();
+ #endif
+ __Pyx_AddTraceback("View.MemoryView.memoryview_copy_contents", __pyx_clineno, __pyx_lineno, __pyx_filename);
+ #ifdef WITH_THREAD
+ PyGILState_Release(__pyx_gilstate_save);
+ #endif
+ }
+ __pyx_r = -1;
+ __pyx_L0:;
+ return __pyx_r;
+}
+
+/* "View.MemoryView":1294
+ *
+ * @cname('__pyx_memoryview_broadcast_leading')
+ * cdef void broadcast_leading(__Pyx_memviewslice *slice, # <<<<<<<<<<<<<<
+ * int ndim,
+ * int ndim_other) nogil:
+ */
+
+static void __pyx_memoryview_broadcast_leading(__Pyx_memviewslice *__pyx_v_slice, int __pyx_v_ndim, int __pyx_v_ndim_other) {
+ int __pyx_v_i;
+ int __pyx_v_offset;
+ int __pyx_t_1;
+ int __pyx_t_2;
+
+ /* "View.MemoryView":1298
+ * int ndim_other) nogil:
+ * cdef int i
+ * cdef int offset = ndim_other - ndim # <<<<<<<<<<<<<<
+ *
+ * for i in range(ndim - 1, -1, -1):
+ */
+ __pyx_v_offset = (__pyx_v_ndim_other - __pyx_v_ndim);
+
+ /* "View.MemoryView":1300
+ * cdef int offset = ndim_other - ndim
+ *
+ * for i in range(ndim - 1, -1, -1): # <<<<<<<<<<<<<<
+ * slice.shape[i + offset] = slice.shape[i]
+ * slice.strides[i + offset] = slice.strides[i]
+ */
+ for (__pyx_t_1 = (__pyx_v_ndim - 1); __pyx_t_1 > -1; __pyx_t_1-=1) {
+ __pyx_v_i = __pyx_t_1;
+
+ /* "View.MemoryView":1301
+ *
+ * for i in range(ndim - 1, -1, -1):
+ * slice.shape[i + offset] = slice.shape[i] # <<<<<<<<<<<<<<
+ * slice.strides[i + offset] = slice.strides[i]
+ * slice.suboffsets[i + offset] = slice.suboffsets[i]
+ */
+ (__pyx_v_slice->shape[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->shape[__pyx_v_i]);
+
+ /* "View.MemoryView":1302
+ * for i in range(ndim - 1, -1, -1):
+ * slice.shape[i + offset] = slice.shape[i]
+ * slice.strides[i + offset] = slice.strides[i] # <<<<<<<<<<<<<<
+ * slice.suboffsets[i + offset] = slice.suboffsets[i]
+ *
+ */
+ (__pyx_v_slice->strides[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->strides[__pyx_v_i]);
+
+ /* "View.MemoryView":1303
+ * slice.shape[i + offset] = slice.shape[i]
+ * slice.strides[i + offset] = slice.strides[i]
+ * slice.suboffsets[i + offset] = slice.suboffsets[i] # <<<<<<<<<<<<<<
+ *
+ * for i in range(offset):
+ */
+ (__pyx_v_slice->suboffsets[(__pyx_v_i + __pyx_v_offset)]) = (__pyx_v_slice->suboffsets[__pyx_v_i]);
+ }
+
+ /* "View.MemoryView":1305
+ * slice.suboffsets[i + offset] = slice.suboffsets[i]
+ *
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+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_10partfinder_6_tiger_TigerDNA, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_10partfinder_6_tiger_TigerDNA, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ 0, /*tp_version_tag*/
+ #if PY_VERSION_HEX >= 0x030400a1
+ 0, /*tp_finalize*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_array(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_array_obj *p;
+ PyObject *o;
+ if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
+ o = (*t->tp_alloc)(t, 0);
+ } else {
+ o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
+ }
+ if (unlikely(!o)) return 0;
+ p = ((struct __pyx_array_obj *)o);
+ p->mode = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ p->_format = ((PyObject*)Py_None); Py_INCREF(Py_None);
+ if (unlikely(__pyx_array___cinit__(o, a, k) < 0)) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static void __pyx_tp_dealloc_array(PyObject *o) {
+ struct __pyx_array_obj *p = (struct __pyx_array_obj *)o;
+ #if PY_VERSION_HEX >= 0x030400a1
+ if (unlikely(Py_TYPE(o)->tp_finalize) && (!PyType_IS_GC(Py_TYPE(o)) || !_PyGC_FINALIZED(o))) {
+ if (PyObject_CallFinalizerFromDealloc(o)) return;
+ }
+ #endif
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_array___dealloc__(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->mode);
+ Py_CLEAR(p->_format);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+static PyObject *__pyx_sq_item_array(PyObject *o, Py_ssize_t i) {
+ PyObject *r;
+ PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
+ r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
+ Py_DECREF(x);
+ return r;
+}
+
+static int __pyx_mp_ass_subscript_array(PyObject *o, PyObject *i, PyObject *v) {
+ if (v) {
+ return __pyx_array___setitem__(o, i, v);
+ }
+ else {
+ PyErr_Format(PyExc_NotImplementedError,
+ "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name);
+ return -1;
+ }
+}
+
+static PyObject *__pyx_tp_getattro_array(PyObject *o, PyObject *n) {
+ PyObject *v = PyObject_GenericGetAttr(o, n);
+ if (!v && PyErr_ExceptionMatches(PyExc_AttributeError)) {
+ PyErr_Clear();
+ v = __pyx_array___getattr__(o, n);
+ }
+ return v;
+}
+
+static PyObject *__pyx_getprop___pyx_array_memview(PyObject *o, CYTHON_UNUSED void *x) {
+ return get_memview(o);
+}
+
+static PyMethodDef __pyx_methods_array[] = {
+ {"__getattr__", (PyCFunction)__pyx_array___getattr__, METH_O|METH_COEXIST, 0},
+ {0, 0, 0, 0}
+};
+
+static struct PyGetSetDef __pyx_getsets_array[] = {
+ {(char *)"memview", __pyx_getprop___pyx_array_memview, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_array = {
+ 0, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ __pyx_sq_item_array, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_array = {
+ 0, /*mp_length*/
+ __pyx_array___getitem__, /*mp_subscript*/
+ __pyx_mp_ass_subscript_array, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_array = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ __pyx_array_getbuffer, /*bf_getbuffer*/
+ 0, /*bf_releasebuffer*/
+};
+
+static PyTypeObject __pyx_type___pyx_array = {
+ PyVarObject_HEAD_INIT(0, 0)
+ "partfinder._tiger.array", /*tp_name*/
+ sizeof(struct __pyx_array_obj), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_array, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ 0, /*tp_repr*/
+ 0, /*tp_as_number*/
+ &__pyx_tp_as_sequence_array, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_array, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ __pyx_tp_getattro_array, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_array, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE, /*tp_flags*/
+ 0, /*tp_doc*/
+ 0, /*tp_traverse*/
+ 0, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_array, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_array, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_array, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ 0, /*tp_version_tag*/
+ #if PY_VERSION_HEX >= 0x030400a1
+ 0, /*tp_finalize*/
+ #endif
+};
+
+static PyObject *__pyx_tp_new_Enum(PyTypeObject *t, CYTHON_UNUSED PyObject *a, CYTHON_UNUSED PyObject *k) {
+ struct __pyx_MemviewEnum_obj *p;
+ PyObject *o;
+ if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
+ o = (*t->tp_alloc)(t, 0);
+ } else {
+ o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
+ }
+ if (unlikely(!o)) return 0;
+ p = ((struct __pyx_MemviewEnum_obj *)o);
+ p->name = Py_None; Py_INCREF(Py_None);
+ return o;
+}
+
+static void __pyx_tp_dealloc_Enum(PyObject *o) {
+ struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o;
+ #if PY_VERSION_HEX >= 0x030400a1
+ if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
+ if (PyObject_CallFinalizerFromDealloc(o)) return;
+ }
+ #endif
+ PyObject_GC_UnTrack(o);
+ Py_CLEAR(p->name);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_Enum(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o;
+ if (p->name) {
+ e = (*v)(p->name, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_Enum(PyObject *o) {
+ PyObject* tmp;
+ struct __pyx_MemviewEnum_obj *p = (struct __pyx_MemviewEnum_obj *)o;
+ tmp = ((PyObject*)p->name);
+ p->name = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ return 0;
+}
+
+static PyMethodDef __pyx_methods_Enum[] = {
+ {0, 0, 0, 0}
+};
+
+static PyTypeObject __pyx_type___pyx_MemviewEnum = {
+ PyVarObject_HEAD_INIT(0, 0)
+ "partfinder._tiger.Enum", /*tp_name*/
+ sizeof(struct __pyx_MemviewEnum_obj), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_Enum, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ __pyx_MemviewEnum___repr__, /*tp_repr*/
+ 0, /*tp_as_number*/
+ 0, /*tp_as_sequence*/
+ 0, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ 0, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ 0, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_Enum, /*tp_traverse*/
+ __pyx_tp_clear_Enum, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_Enum, /*tp_methods*/
+ 0, /*tp_members*/
+ 0, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ __pyx_MemviewEnum___init__, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_Enum, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ 0, /*tp_version_tag*/
+ #if PY_VERSION_HEX >= 0x030400a1
+ 0, /*tp_finalize*/
+ #endif
+};
+static struct __pyx_vtabstruct_memoryview __pyx_vtable_memoryview;
+
+static PyObject *__pyx_tp_new_memoryview(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_memoryview_obj *p;
+ PyObject *o;
+ if (likely((t->tp_flags & Py_TPFLAGS_IS_ABSTRACT) == 0)) {
+ o = (*t->tp_alloc)(t, 0);
+ } else {
+ o = (PyObject *) PyBaseObject_Type.tp_new(t, __pyx_empty_tuple, 0);
+ }
+ if (unlikely(!o)) return 0;
+ p = ((struct __pyx_memoryview_obj *)o);
+ p->__pyx_vtab = __pyx_vtabptr_memoryview;
+ p->obj = Py_None; Py_INCREF(Py_None);
+ p->_size = Py_None; Py_INCREF(Py_None);
+ p->_array_interface = Py_None; Py_INCREF(Py_None);
+ p->view.obj = NULL;
+ if (unlikely(__pyx_memoryview___cinit__(o, a, k) < 0)) {
+ Py_DECREF(o); o = 0;
+ }
+ return o;
+}
+
+static void __pyx_tp_dealloc_memoryview(PyObject *o) {
+ struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o;
+ #if PY_VERSION_HEX >= 0x030400a1
+ if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
+ if (PyObject_CallFinalizerFromDealloc(o)) return;
+ }
+ #endif
+ PyObject_GC_UnTrack(o);
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_memoryview___dealloc__(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->obj);
+ Py_CLEAR(p->_size);
+ Py_CLEAR(p->_array_interface);
+ (*Py_TYPE(o)->tp_free)(o);
+}
+
+static int __pyx_tp_traverse_memoryview(PyObject *o, visitproc v, void *a) {
+ int e;
+ struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o;
+ if (p->obj) {
+ e = (*v)(p->obj, a); if (e) return e;
+ }
+ if (p->_size) {
+ e = (*v)(p->_size, a); if (e) return e;
+ }
+ if (p->_array_interface) {
+ e = (*v)(p->_array_interface, a); if (e) return e;
+ }
+ if (p->view.obj) {
+ e = (*v)(p->view.obj, a); if (e) return e;
+ }
+ return 0;
+}
+
+static int __pyx_tp_clear_memoryview(PyObject *o) {
+ PyObject* tmp;
+ struct __pyx_memoryview_obj *p = (struct __pyx_memoryview_obj *)o;
+ tmp = ((PyObject*)p->obj);
+ p->obj = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->_size);
+ p->_size = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ tmp = ((PyObject*)p->_array_interface);
+ p->_array_interface = Py_None; Py_INCREF(Py_None);
+ Py_XDECREF(tmp);
+ Py_CLEAR(p->view.obj);
+ return 0;
+}
+static PyObject *__pyx_sq_item_memoryview(PyObject *o, Py_ssize_t i) {
+ PyObject *r;
+ PyObject *x = PyInt_FromSsize_t(i); if(!x) return 0;
+ r = Py_TYPE(o)->tp_as_mapping->mp_subscript(o, x);
+ Py_DECREF(x);
+ return r;
+}
+
+static int __pyx_mp_ass_subscript_memoryview(PyObject *o, PyObject *i, PyObject *v) {
+ if (v) {
+ return __pyx_memoryview___setitem__(o, i, v);
+ }
+ else {
+ PyErr_Format(PyExc_NotImplementedError,
+ "Subscript deletion not supported by %.200s", Py_TYPE(o)->tp_name);
+ return -1;
+ }
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_T(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_transpose(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_base(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview__get__base(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_shape(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_shape(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_strides(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_strides(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_suboffsets(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_suboffsets(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_ndim(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_ndim(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_itemsize(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_itemsize(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_nbytes(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_nbytes(o);
+}
+
+static PyObject *__pyx_getprop___pyx_memoryview_size(PyObject *o, CYTHON_UNUSED void *x) {
+ return __pyx_memoryview_get_size(o);
+}
+
+static PyMethodDef __pyx_methods_memoryview[] = {
+ {"is_c_contig", (PyCFunction)__pyx_memoryview_is_c_contig, METH_NOARGS, 0},
+ {"is_f_contig", (PyCFunction)__pyx_memoryview_is_f_contig, METH_NOARGS, 0},
+ {"copy", (PyCFunction)__pyx_memoryview_copy, METH_NOARGS, 0},
+ {"copy_fortran", (PyCFunction)__pyx_memoryview_copy_fortran, METH_NOARGS, 0},
+ {0, 0, 0, 0}
+};
+
+static struct PyGetSetDef __pyx_getsets_memoryview[] = {
+ {(char *)"T", __pyx_getprop___pyx_memoryview_T, 0, 0, 0},
+ {(char *)"base", __pyx_getprop___pyx_memoryview_base, 0, 0, 0},
+ {(char *)"shape", __pyx_getprop___pyx_memoryview_shape, 0, 0, 0},
+ {(char *)"strides", __pyx_getprop___pyx_memoryview_strides, 0, 0, 0},
+ {(char *)"suboffsets", __pyx_getprop___pyx_memoryview_suboffsets, 0, 0, 0},
+ {(char *)"ndim", __pyx_getprop___pyx_memoryview_ndim, 0, 0, 0},
+ {(char *)"itemsize", __pyx_getprop___pyx_memoryview_itemsize, 0, 0, 0},
+ {(char *)"nbytes", __pyx_getprop___pyx_memoryview_nbytes, 0, 0, 0},
+ {(char *)"size", __pyx_getprop___pyx_memoryview_size, 0, 0, 0},
+ {0, 0, 0, 0, 0}
+};
+
+static PySequenceMethods __pyx_tp_as_sequence_memoryview = {
+ __pyx_memoryview___len__, /*sq_length*/
+ 0, /*sq_concat*/
+ 0, /*sq_repeat*/
+ __pyx_sq_item_memoryview, /*sq_item*/
+ 0, /*sq_slice*/
+ 0, /*sq_ass_item*/
+ 0, /*sq_ass_slice*/
+ 0, /*sq_contains*/
+ 0, /*sq_inplace_concat*/
+ 0, /*sq_inplace_repeat*/
+};
+
+static PyMappingMethods __pyx_tp_as_mapping_memoryview = {
+ __pyx_memoryview___len__, /*mp_length*/
+ __pyx_memoryview___getitem__, /*mp_subscript*/
+ __pyx_mp_ass_subscript_memoryview, /*mp_ass_subscript*/
+};
+
+static PyBufferProcs __pyx_tp_as_buffer_memoryview = {
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getreadbuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getwritebuffer*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getsegcount*/
+ #endif
+ #if PY_MAJOR_VERSION < 3
+ 0, /*bf_getcharbuffer*/
+ #endif
+ __pyx_memoryview_getbuffer, /*bf_getbuffer*/
+ 0, /*bf_releasebuffer*/
+};
+
+static PyTypeObject __pyx_type___pyx_memoryview = {
+ PyVarObject_HEAD_INIT(0, 0)
+ "partfinder._tiger.memoryview", /*tp_name*/
+ sizeof(struct __pyx_memoryview_obj), /*tp_basicsize*/
+ 0, /*tp_itemsize*/
+ __pyx_tp_dealloc_memoryview, /*tp_dealloc*/
+ 0, /*tp_print*/
+ 0, /*tp_getattr*/
+ 0, /*tp_setattr*/
+ #if PY_MAJOR_VERSION < 3
+ 0, /*tp_compare*/
+ #else
+ 0, /*reserved*/
+ #endif
+ __pyx_memoryview___repr__, /*tp_repr*/
+ 0, /*tp_as_number*/
+ &__pyx_tp_as_sequence_memoryview, /*tp_as_sequence*/
+ &__pyx_tp_as_mapping_memoryview, /*tp_as_mapping*/
+ 0, /*tp_hash*/
+ 0, /*tp_call*/
+ __pyx_memoryview___str__, /*tp_str*/
+ 0, /*tp_getattro*/
+ 0, /*tp_setattro*/
+ &__pyx_tp_as_buffer_memoryview, /*tp_as_buffer*/
+ Py_TPFLAGS_DEFAULT|Py_TPFLAGS_HAVE_VERSION_TAG|Py_TPFLAGS_CHECKTYPES|Py_TPFLAGS_HAVE_NEWBUFFER|Py_TPFLAGS_BASETYPE|Py_TPFLAGS_HAVE_GC, /*tp_flags*/
+ 0, /*tp_doc*/
+ __pyx_tp_traverse_memoryview, /*tp_traverse*/
+ __pyx_tp_clear_memoryview, /*tp_clear*/
+ 0, /*tp_richcompare*/
+ 0, /*tp_weaklistoffset*/
+ 0, /*tp_iter*/
+ 0, /*tp_iternext*/
+ __pyx_methods_memoryview, /*tp_methods*/
+ 0, /*tp_members*/
+ __pyx_getsets_memoryview, /*tp_getset*/
+ 0, /*tp_base*/
+ 0, /*tp_dict*/
+ 0, /*tp_descr_get*/
+ 0, /*tp_descr_set*/
+ 0, /*tp_dictoffset*/
+ 0, /*tp_init*/
+ 0, /*tp_alloc*/
+ __pyx_tp_new_memoryview, /*tp_new*/
+ 0, /*tp_free*/
+ 0, /*tp_is_gc*/
+ 0, /*tp_bases*/
+ 0, /*tp_mro*/
+ 0, /*tp_cache*/
+ 0, /*tp_subclasses*/
+ 0, /*tp_weaklist*/
+ 0, /*tp_del*/
+ 0, /*tp_version_tag*/
+ #if PY_VERSION_HEX >= 0x030400a1
+ 0, /*tp_finalize*/
+ #endif
+};
+static struct __pyx_vtabstruct__memoryviewslice __pyx_vtable__memoryviewslice;
+
+static PyObject *__pyx_tp_new__memoryviewslice(PyTypeObject *t, PyObject *a, PyObject *k) {
+ struct __pyx_memoryviewslice_obj *p;
+ PyObject *o = __pyx_tp_new_memoryview(t, a, k);
+ if (unlikely(!o)) return 0;
+ p = ((struct __pyx_memoryviewslice_obj *)o);
+ p->__pyx_base.__pyx_vtab = (struct __pyx_vtabstruct_memoryview*)__pyx_vtabptr__memoryviewslice;
+ p->from_object = Py_None; Py_INCREF(Py_None);
+ p->from_slice.memview = NULL;
+ return o;
+}
+
+static void __pyx_tp_dealloc__memoryviewslice(PyObject *o) {
+ struct __pyx_memoryviewslice_obj *p = (struct __pyx_memoryviewslice_obj *)o;
+ #if PY_VERSION_HEX >= 0x030400a1
+ if (unlikely(Py_TYPE(o)->tp_finalize) && !_PyGC_FINALIZED(o)) {
+ if (PyObject_CallFinalizerFromDealloc(o)) return;
+ }
+ #endif
+ PyObject_GC_UnTrack(o);
+ {
+ PyObject *etype, *eval, *etb;
+ PyErr_Fetch(&etype, &eval, &etb);
+ ++Py_REFCNT(o);
+ __pyx_memoryviewslice___dealloc__(o);
+ --Py_REFCNT(o);
+ PyErr_Restore(etype, eval, etb);
+ }
+ Py_CLEAR(p->from_object);
+ PyObject_GC_Track(o);
+ __pyx_tp_dealloc_memoryview(o);
+}
+
+static int __pyx_tp_traverse__memoryviewslice(PyObject *o, visitproc v, void *a) {
+ int e;
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+ #ifdef WITH_THREAD /* Python build with threading support? */
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+ #endif
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+static size_t __Pyx_BufFmt_TypeCharToAlignment(char ch, CYTHON_UNUSED int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return sizeof(__Pyx_st_short) - sizeof(short);
+ case 'i': case 'I': return sizeof(__Pyx_st_int) - sizeof(int);
+ case 'l': case 'L': return sizeof(__Pyx_st_long) - sizeof(long);
+#ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(__Pyx_st_longlong) - sizeof(PY_LONG_LONG);
+#endif
+ case 'f': return sizeof(__Pyx_st_float) - sizeof(float);
+ case 'd': return sizeof(__Pyx_st_double) - sizeof(double);
+ case 'g': return sizeof(__Pyx_st_longdouble) - sizeof(long double);
+ case 'P': case 'O': return sizeof(__Pyx_st_void_p) - sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+/* These are for computing the padding at the end of the struct to align
+ on the first member of the struct. This will probably the same as above,
+ but we don't have any guarantees.
+ */
+typedef struct { short x; char c; } __Pyx_pad_short;
+typedef struct { int x; char c; } __Pyx_pad_int;
+typedef struct { long x; char c; } __Pyx_pad_long;
+typedef struct { float x; char c; } __Pyx_pad_float;
+typedef struct { double x; char c; } __Pyx_pad_double;
+typedef struct { long double x; char c; } __Pyx_pad_longdouble;
+typedef struct { void *x; char c; } __Pyx_pad_void_p;
+#ifdef HAVE_LONG_LONG
+typedef struct { PY_LONG_LONG x; char c; } __Pyx_pad_longlong;
+#endif
+static size_t __Pyx_BufFmt_TypeCharToPadding(char ch, CYTHON_UNUSED int is_complex) {
+ switch (ch) {
+ case '?': case 'c': case 'b': case 'B': case 's': case 'p': return 1;
+ case 'h': case 'H': return sizeof(__Pyx_pad_short) - sizeof(short);
+ case 'i': case 'I': return sizeof(__Pyx_pad_int) - sizeof(int);
+ case 'l': case 'L': return sizeof(__Pyx_pad_long) - sizeof(long);
+#ifdef HAVE_LONG_LONG
+ case 'q': case 'Q': return sizeof(__Pyx_pad_longlong) - sizeof(PY_LONG_LONG);
+#endif
+ case 'f': return sizeof(__Pyx_pad_float) - sizeof(float);
+ case 'd': return sizeof(__Pyx_pad_double) - sizeof(double);
+ case 'g': return sizeof(__Pyx_pad_longdouble) - sizeof(long double);
+ case 'P': case 'O': return sizeof(__Pyx_pad_void_p) - sizeof(void*);
+ default:
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+}
+static char __Pyx_BufFmt_TypeCharToGroup(char ch, int is_complex) {
+ switch (ch) {
+ case 'c':
+ return 'H';
+ case 'b': case 'h': case 'i':
+ case 'l': case 'q': case 's': case 'p':
+ return 'I';
+ case 'B': case 'H': case 'I': case 'L': case 'Q':
+ return 'U';
+ case 'f': case 'd': case 'g':
+ return (is_complex ? 'C' : 'R');
+ case 'O':
+ return 'O';
+ case 'P':
+ return 'P';
+ default: {
+ __Pyx_BufFmt_RaiseUnexpectedChar(ch);
+ return 0;
+ }
+ }
+}
+static void __Pyx_BufFmt_RaiseExpected(__Pyx_BufFmt_Context* ctx) {
+ if (ctx->head == NULL || ctx->head->field == &ctx->root) {
+ const char* expected;
+ const char* quote;
+ if (ctx->head == NULL) {
+ expected = "end";
+ quote = "";
+ } else {
+ expected = ctx->head->field->type->name;
+ quote = "'";
+ }
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch, expected %s%s%s but got %s",
+ quote, expected, quote,
+ __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex));
+ } else {
+ __Pyx_StructField* field = ctx->head->field;
+ __Pyx_StructField* parent = (ctx->head - 1)->field;
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch, expected '%s' but got %s in '%s.%s'",
+ field->type->name, __Pyx_BufFmt_DescribeTypeChar(ctx->enc_type, ctx->is_complex),
+ parent->type->name, field->name);
+ }
+}
+static int __Pyx_BufFmt_ProcessTypeChunk(__Pyx_BufFmt_Context* ctx) {
+ char group;
+ size_t size, offset, arraysize = 1;
+ if (ctx->enc_type == 0) return 0;
+ if (ctx->head->field->type->arraysize[0]) {
+ int i, ndim = 0;
+ if (ctx->enc_type == 's' || ctx->enc_type == 'p') {
+ ctx->is_valid_array = ctx->head->field->type->ndim == 1;
+ ndim = 1;
+ if (ctx->enc_count != ctx->head->field->type->arraysize[0]) {
+ PyErr_Format(PyExc_ValueError,
+ "Expected a dimension of size %zu, got %zu",
+ ctx->head->field->type->arraysize[0], ctx->enc_count);
+ return -1;
+ }
+ }
+ if (!ctx->is_valid_array) {
+ PyErr_Format(PyExc_ValueError, "Expected %d dimensions, got %d",
+ ctx->head->field->type->ndim, ndim);
+ return -1;
+ }
+ for (i = 0; i < ctx->head->field->type->ndim; i++) {
+ arraysize *= ctx->head->field->type->arraysize[i];
+ }
+ ctx->is_valid_array = 0;
+ ctx->enc_count = 1;
+ }
+ group = __Pyx_BufFmt_TypeCharToGroup(ctx->enc_type, ctx->is_complex);
+ do {
+ __Pyx_StructField* field = ctx->head->field;
+ __Pyx_TypeInfo* type = field->type;
+ if (ctx->enc_packmode == '@' || ctx->enc_packmode == '^') {
+ size = __Pyx_BufFmt_TypeCharToNativeSize(ctx->enc_type, ctx->is_complex);
+ } else {
+ size = __Pyx_BufFmt_TypeCharToStandardSize(ctx->enc_type, ctx->is_complex);
+ }
+ if (ctx->enc_packmode == '@') {
+ size_t align_at = __Pyx_BufFmt_TypeCharToAlignment(ctx->enc_type, ctx->is_complex);
+ size_t align_mod_offset;
+ if (align_at == 0) return -1;
+ align_mod_offset = ctx->fmt_offset % align_at;
+ if (align_mod_offset > 0) ctx->fmt_offset += align_at - align_mod_offset;
+ if (ctx->struct_alignment == 0)
+ ctx->struct_alignment = __Pyx_BufFmt_TypeCharToPadding(ctx->enc_type,
+ ctx->is_complex);
+ }
+ if (type->size != size || type->typegroup != group) {
+ if (type->typegroup == 'C' && type->fields != NULL) {
+ size_t parent_offset = ctx->head->parent_offset + field->offset;
+ ++ctx->head;
+ ctx->head->field = type->fields;
+ ctx->head->parent_offset = parent_offset;
+ continue;
+ }
+ if ((type->typegroup == 'H' || group == 'H') && type->size == size) {
+ } else {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
+ }
+ }
+ offset = ctx->head->parent_offset + field->offset;
+ if (ctx->fmt_offset != offset) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer dtype mismatch; next field is at offset %" CYTHON_FORMAT_SSIZE_T "d but %" CYTHON_FORMAT_SSIZE_T "d expected",
+ (Py_ssize_t)ctx->fmt_offset, (Py_ssize_t)offset);
+ return -1;
+ }
+ ctx->fmt_offset += size;
+ if (arraysize)
+ ctx->fmt_offset += (arraysize - 1) * size;
+ --ctx->enc_count;
+ while (1) {
+ if (field == &ctx->root) {
+ ctx->head = NULL;
+ if (ctx->enc_count != 0) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return -1;
+ }
+ break;
+ }
+ ctx->head->field = ++field;
+ if (field->type == NULL) {
+ --ctx->head;
+ field = ctx->head->field;
+ continue;
+ } else if (field->type->typegroup == 'S') {
+ size_t parent_offset = ctx->head->parent_offset + field->offset;
+ if (field->type->fields->type == NULL) continue;
+ field = field->type->fields;
+ ++ctx->head;
+ ctx->head->field = field;
+ ctx->head->parent_offset = parent_offset;
+ break;
+ } else {
+ break;
+ }
+ }
+ } while (ctx->enc_count);
+ ctx->enc_type = 0;
+ ctx->is_complex = 0;
+ return 0;
+}
+static CYTHON_INLINE PyObject *
+__pyx_buffmt_parse_array(__Pyx_BufFmt_Context* ctx, const char** tsp)
+{
+ const char *ts = *tsp;
+ int i = 0, number;
+ int ndim = ctx->head->field->type->ndim;
+;
+ ++ts;
+ if (ctx->new_count != 1) {
+ PyErr_SetString(PyExc_ValueError,
+ "Cannot handle repeated arrays in format string");
+ return NULL;
+ }
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ while (*ts && *ts != ')') {
+ switch (*ts) {
+ case ' ': case '\f': case '\r': case '\n': case '\t': case '\v': continue;
+ default: break;
+ }
+ number = __Pyx_BufFmt_ExpectNumber(&ts);
+ if (number == -1) return NULL;
+ if (i < ndim && (size_t) number != ctx->head->field->type->arraysize[i])
+ return PyErr_Format(PyExc_ValueError,
+ "Expected a dimension of size %zu, got %d",
+ ctx->head->field->type->arraysize[i], number);
+ if (*ts != ',' && *ts != ')')
+ return PyErr_Format(PyExc_ValueError,
+ "Expected a comma in format string, got '%c'", *ts);
+ if (*ts == ',') ts++;
+ i++;
+ }
+ if (i != ndim)
+ return PyErr_Format(PyExc_ValueError, "Expected %d dimension(s), got %d",
+ ctx->head->field->type->ndim, i);
+ if (!*ts) {
+ PyErr_SetString(PyExc_ValueError,
+ "Unexpected end of format string, expected ')'");
+ return NULL;
+ }
+ ctx->is_valid_array = 1;
+ ctx->new_count = 1;
+ *tsp = ++ts;
+ return Py_None;
+}
+static const char* __Pyx_BufFmt_CheckString(__Pyx_BufFmt_Context* ctx, const char* ts) {
+ int got_Z = 0;
+ while (1) {
+ switch(*ts) {
+ case 0:
+ if (ctx->enc_type != 0 && ctx->head == NULL) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return NULL;
+ }
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ if (ctx->head != NULL) {
+ __Pyx_BufFmt_RaiseExpected(ctx);
+ return NULL;
+ }
+ return ts;
+ case ' ':
+ case '\r':
+ case '\n':
+ ++ts;
+ break;
+ case '<':
+ if (!__Pyx_IsLittleEndian()) {
+ PyErr_SetString(PyExc_ValueError, "Little-endian buffer not supported on big-endian compiler");
+ return NULL;
+ }
+ ctx->new_packmode = '=';
+ ++ts;
+ break;
+ case '>':
+ case '!':
+ if (__Pyx_IsLittleEndian()) {
+ PyErr_SetString(PyExc_ValueError, "Big-endian buffer not supported on little-endian compiler");
+ return NULL;
+ }
+ ctx->new_packmode = '=';
+ ++ts;
+ break;
+ case '=':
+ case '@':
+ case '^':
+ ctx->new_packmode = *ts++;
+ break;
+ case 'T':
+ {
+ const char* ts_after_sub;
+ size_t i, struct_count = ctx->new_count;
+ size_t struct_alignment = ctx->struct_alignment;
+ ctx->new_count = 1;
+ ++ts;
+ if (*ts != '{') {
+ PyErr_SetString(PyExc_ValueError, "Buffer acquisition: Expected '{' after 'T'");
+ return NULL;
+ }
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_type = 0;
+ ctx->enc_count = 0;
+ ctx->struct_alignment = 0;
+ ++ts;
+ ts_after_sub = ts;
+ for (i = 0; i != struct_count; ++i) {
+ ts_after_sub = __Pyx_BufFmt_CheckString(ctx, ts);
+ if (!ts_after_sub) return NULL;
+ }
+ ts = ts_after_sub;
+ if (struct_alignment) ctx->struct_alignment = struct_alignment;
+ }
+ break;
+ case '}':
+ {
+ size_t alignment = ctx->struct_alignment;
+ ++ts;
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_type = 0;
+ if (alignment && ctx->fmt_offset % alignment) {
+ ctx->fmt_offset += alignment - (ctx->fmt_offset % alignment);
+ }
+ }
+ return ts;
+ case 'x':
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->fmt_offset += ctx->new_count;
+ ctx->new_count = 1;
+ ctx->enc_count = 0;
+ ctx->enc_type = 0;
+ ctx->enc_packmode = ctx->new_packmode;
+ ++ts;
+ break;
+ case 'Z':
+ got_Z = 1;
+ ++ts;
+ if (*ts != 'f' && *ts != 'd' && *ts != 'g') {
+ __Pyx_BufFmt_RaiseUnexpectedChar('Z');
+ return NULL;
+ }
+ case 'c': case 'b': case 'B': case 'h': case 'H': case 'i': case 'I':
+ case 'l': case 'L': case 'q': case 'Q':
+ case 'f': case 'd': case 'g':
+ case 'O': case 'p':
+ if (ctx->enc_type == *ts && got_Z == ctx->is_complex &&
+ ctx->enc_packmode == ctx->new_packmode) {
+ ctx->enc_count += ctx->new_count;
+ ctx->new_count = 1;
+ got_Z = 0;
+ ++ts;
+ break;
+ }
+ case 's':
+ if (__Pyx_BufFmt_ProcessTypeChunk(ctx) == -1) return NULL;
+ ctx->enc_count = ctx->new_count;
+ ctx->enc_packmode = ctx->new_packmode;
+ ctx->enc_type = *ts;
+ ctx->is_complex = got_Z;
+ ++ts;
+ ctx->new_count = 1;
+ got_Z = 0;
+ break;
+ case ':':
+ ++ts;
+ while(*ts != ':') ++ts;
+ ++ts;
+ break;
+ case '(':
+ if (!__pyx_buffmt_parse_array(ctx, &ts)) return NULL;
+ break;
+ default:
+ {
+ int number = __Pyx_BufFmt_ExpectNumber(&ts);
+ if (number == -1) return NULL;
+ ctx->new_count = (size_t)number;
+ }
+ }
+ }
+}
+static CYTHON_INLINE void __Pyx_ZeroBuffer(Py_buffer* buf) {
+ buf->buf = NULL;
+ buf->obj = NULL;
+ buf->strides = __Pyx_zeros;
+ buf->shape = __Pyx_zeros;
+ buf->suboffsets = __Pyx_minusones;
+}
+static CYTHON_INLINE int __Pyx_GetBufferAndValidate(
+ Py_buffer* buf, PyObject* obj, __Pyx_TypeInfo* dtype, int flags,
+ int nd, int cast, __Pyx_BufFmt_StackElem* stack)
+{
+ if (obj == Py_None || obj == NULL) {
+ __Pyx_ZeroBuffer(buf);
+ return 0;
+ }
+ buf->buf = NULL;
+ if (__Pyx_GetBuffer(obj, buf, flags) == -1) goto fail;
+ if (buf->ndim != nd) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer has wrong number of dimensions (expected %d, got %d)",
+ nd, buf->ndim);
+ goto fail;
+ }
+ if (!cast) {
+ __Pyx_BufFmt_Context ctx;
+ __Pyx_BufFmt_Init(&ctx, stack, dtype);
+ if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
+ }
+ if ((unsigned)buf->itemsize != dtype->size) {
+ PyErr_Format(PyExc_ValueError,
+ "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "d byte%s) does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "d byte%s)",
+ buf->itemsize, (buf->itemsize > 1) ? "s" : "",
+ dtype->name, (Py_ssize_t)dtype->size, (dtype->size > 1) ? "s" : "");
+ goto fail;
+ }
+ if (buf->suboffsets == NULL) buf->suboffsets = __Pyx_minusones;
+ return 0;
+fail:;
+ __Pyx_ZeroBuffer(buf);
+ return -1;
+}
+static CYTHON_INLINE void __Pyx_SafeReleaseBuffer(Py_buffer* info) {
+ if (info->buf == NULL) return;
+ if (info->suboffsets == __Pyx_minusones) info->suboffsets = NULL;
+ __Pyx_ReleaseBuffer(info);
+}
+
+static int
+__Pyx_init_memviewslice(struct __pyx_memoryview_obj *memview,
+ int ndim,
+ __Pyx_memviewslice *memviewslice,
+ int memview_is_new_reference)
+{
+ __Pyx_RefNannyDeclarations
+ int i, retval=-1;
+ Py_buffer *buf = &memview->view;
+ __Pyx_RefNannySetupContext("init_memviewslice", 0);
+ if (!buf) {
+ PyErr_SetString(PyExc_ValueError,
+ "buf is NULL.");
+ goto fail;
+ } else if (memviewslice->memview || memviewslice->data) {
+ PyErr_SetString(PyExc_ValueError,
+ "memviewslice is already initialized!");
+ goto fail;
+ }
+ if (buf->strides) {
+ for (i = 0; i < ndim; i++) {
+ memviewslice->strides[i] = buf->strides[i];
+ }
+ } else {
+ Py_ssize_t stride = buf->itemsize;
+ for (i = ndim - 1; i >= 0; i--) {
+ memviewslice->strides[i] = stride;
+ stride *= buf->shape[i];
+ }
+ }
+ for (i = 0; i < ndim; i++) {
+ memviewslice->shape[i] = buf->shape[i];
+ if (buf->suboffsets) {
+ memviewslice->suboffsets[i] = buf->suboffsets[i];
+ } else {
+ memviewslice->suboffsets[i] = -1;
+ }
+ }
+ memviewslice->memview = memview;
+ memviewslice->data = (char *)buf->buf;
+ if (__pyx_add_acquisition_count(memview) == 0 && !memview_is_new_reference) {
+ Py_INCREF(memview);
+ }
+ retval = 0;
+ goto no_fail;
+fail:
+ memviewslice->memview = 0;
+ memviewslice->data = 0;
+ retval = -1;
+no_fail:
+ __Pyx_RefNannyFinishContext();
+ return retval;
+}
+static CYTHON_INLINE void __pyx_fatalerror(const char *fmt, ...) {
+ va_list vargs;
+ char msg[200];
+ va_start(vargs, fmt);
+#ifdef HAVE_STDARG_PROTOTYPES
+ va_start(vargs, fmt);
+#else
+ va_start(vargs);
+#endif
+ vsnprintf(msg, 200, fmt, vargs);
+ Py_FatalError(msg);
+ va_end(vargs);
+}
+static CYTHON_INLINE int
+__pyx_add_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
+ PyThread_type_lock lock)
+{
+ int result;
+ PyThread_acquire_lock(lock, 1);
+ result = (*acquisition_count)++;
+ PyThread_release_lock(lock);
+ return result;
+}
+static CYTHON_INLINE int
+__pyx_sub_acquisition_count_locked(__pyx_atomic_int *acquisition_count,
+ PyThread_type_lock lock)
+{
+ int result;
+ PyThread_acquire_lock(lock, 1);
+ result = (*acquisition_count)--;
+ PyThread_release_lock(lock);
+ return result;
+}
+static CYTHON_INLINE void
+__Pyx_INC_MEMVIEW(__Pyx_memviewslice *memslice, int have_gil, int lineno)
+{
+ int first_time;
+ struct __pyx_memoryview_obj *memview = memslice->memview;
+ if (!memview || (PyObject *) memview == Py_None)
+ return;
+ if (__pyx_get_slice_count(memview) < 0)
+ __pyx_fatalerror("Acquisition count is %d (line %d)",
+ __pyx_get_slice_count(memview), lineno);
+ first_time = __pyx_add_acquisition_count(memview) == 0;
+ if (first_time) {
+ if (have_gil) {
+ Py_INCREF((PyObject *) memview);
+ } else {
+ PyGILState_STATE _gilstate = PyGILState_Ensure();
+ Py_INCREF((PyObject *) memview);
+ PyGILState_Release(_gilstate);
+ }
+ }
+}
+static CYTHON_INLINE void __Pyx_XDEC_MEMVIEW(__Pyx_memviewslice *memslice,
+ int have_gil, int lineno) {
+ int last_time;
+ struct __pyx_memoryview_obj *memview = memslice->memview;
+ if (!memview ) {
+ return;
+ } else if ((PyObject *) memview == Py_None) {
+ memslice->memview = NULL;
+ return;
+ }
+ if (__pyx_get_slice_count(memview) <= 0)
+ __pyx_fatalerror("Acquisition count is %d (line %d)",
+ __pyx_get_slice_count(memview), lineno);
+ last_time = __pyx_sub_acquisition_count(memview) == 1;
+ memslice->data = NULL;
+ if (last_time) {
+ if (have_gil) {
+ Py_CLEAR(memslice->memview);
+ } else {
+ PyGILState_STATE _gilstate = PyGILState_Ensure();
+ Py_CLEAR(memslice->memview);
+ PyGILState_Release(_gilstate);
+ }
+ } else {
+ memslice->memview = NULL;
+ }
+}
+
+static CYTHON_INLINE void __Pyx_RaiseTooManyValuesError(Py_ssize_t expected) {
+ PyErr_Format(PyExc_ValueError,
+ "too many values to unpack (expected %" CYTHON_FORMAT_SSIZE_T "d)", expected);
+}
+
+static CYTHON_INLINE void __Pyx_RaiseNeedMoreValuesError(Py_ssize_t index) {
+ PyErr_Format(PyExc_ValueError,
+ "need more than %" CYTHON_FORMAT_SSIZE_T "d value%.1s to unpack",
+ index, (index == 1) ? "" : "s");
+}
+
+static CYTHON_INLINE int __Pyx_IterFinish(void) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* exc_type = tstate->curexc_type;
+ if (unlikely(exc_type)) {
+ if (likely(exc_type == PyExc_StopIteration) || PyErr_GivenExceptionMatches(exc_type, PyExc_StopIteration)) {
+ PyObject *exc_value, *exc_tb;
+ exc_value = tstate->curexc_value;
+ exc_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+ Py_DECREF(exc_type);
+ Py_XDECREF(exc_value);
+ Py_XDECREF(exc_tb);
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#else
+ if (unlikely(PyErr_Occurred())) {
+ if (likely(PyErr_ExceptionMatches(PyExc_StopIteration))) {
+ PyErr_Clear();
+ return 0;
+ } else {
+ return -1;
+ }
+ }
+ return 0;
+#endif
+}
+
+static int __Pyx_IternextUnpackEndCheck(PyObject *retval, Py_ssize_t expected) {
+ if (unlikely(retval)) {
+ Py_DECREF(retval);
+ __Pyx_RaiseTooManyValuesError(expected);
+ return -1;
+ } else {
+ return __Pyx_IterFinish();
+ }
+ return 0;
+}
+
+static CYTHON_INLINE void __Pyx_ErrRestore(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->curexc_type;
+ tmp_value = tstate->curexc_value;
+ tmp_tb = tstate->curexc_traceback;
+ tstate->curexc_type = type;
+ tstate->curexc_value = value;
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_Restore(type, value, tb);
+#endif
+}
+static CYTHON_INLINE void __Pyx_ErrFetch(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->curexc_type;
+ *value = tstate->curexc_value;
+ *tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(type, value, tb);
+#endif
+}
+
+#if PY_MAJOR_VERSION < 3
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb,
+ CYTHON_UNUSED PyObject *cause) {
+ Py_XINCREF(type);
+ if (!value || value == Py_None)
+ value = NULL;
+ else
+ Py_INCREF(value);
+ if (!tb || tb == Py_None)
+ tb = NULL;
+ else {
+ Py_INCREF(tb);
+ if (!PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto raise_error;
+ }
+ }
+ if (PyType_Check(type)) {
+#if CYTHON_COMPILING_IN_PYPY
+ if (!value) {
+ Py_INCREF(Py_None);
+ value = Py_None;
+ }
+#endif
+ PyErr_NormalizeException(&type, &value, &tb);
+ } else {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto raise_error;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(type);
+ Py_INCREF(type);
+ if (!PyType_IsSubtype((PyTypeObject *)type, (PyTypeObject *)PyExc_BaseException)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto raise_error;
+ }
+ }
+ __Pyx_ErrRestore(type, value, tb);
+ return;
+raise_error:
+ Py_XDECREF(value);
+ Py_XDECREF(type);
+ Py_XDECREF(tb);
+ return;
+}
+#else
+static void __Pyx_Raise(PyObject *type, PyObject *value, PyObject *tb, PyObject *cause) {
+ PyObject* owned_instance = NULL;
+ if (tb == Py_None) {
+ tb = 0;
+ } else if (tb && !PyTraceBack_Check(tb)) {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: arg 3 must be a traceback or None");
+ goto bad;
+ }
+ if (value == Py_None)
+ value = 0;
+ if (PyExceptionInstance_Check(type)) {
+ if (value) {
+ PyErr_SetString(PyExc_TypeError,
+ "instance exception may not have a separate value");
+ goto bad;
+ }
+ value = type;
+ type = (PyObject*) Py_TYPE(value);
+ } else if (PyExceptionClass_Check(type)) {
+ PyObject *instance_class = NULL;
+ if (value && PyExceptionInstance_Check(value)) {
+ instance_class = (PyObject*) Py_TYPE(value);
+ if (instance_class != type) {
+ if (PyObject_IsSubclass(instance_class, type)) {
+ type = instance_class;
+ } else {
+ instance_class = NULL;
+ }
+ }
+ }
+ if (!instance_class) {
+ PyObject *args;
+ if (!value)
+ args = PyTuple_New(0);
+ else if (PyTuple_Check(value)) {
+ Py_INCREF(value);
+ args = value;
+ } else
+ args = PyTuple_Pack(1, value);
+ if (!args)
+ goto bad;
+ owned_instance = PyObject_Call(type, args, NULL);
+ Py_DECREF(args);
+ if (!owned_instance)
+ goto bad;
+ value = owned_instance;
+ if (!PyExceptionInstance_Check(value)) {
+ PyErr_Format(PyExc_TypeError,
+ "calling %R should have returned an instance of "
+ "BaseException, not %R",
+ type, Py_TYPE(value));
+ goto bad;
+ }
+ }
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "raise: exception class must be a subclass of BaseException");
+ goto bad;
+ }
+#if PY_VERSION_HEX >= 0x03030000
+ if (cause) {
+#else
+ if (cause && cause != Py_None) {
+#endif
+ PyObject *fixed_cause;
+ if (cause == Py_None) {
+ fixed_cause = NULL;
+ } else if (PyExceptionClass_Check(cause)) {
+ fixed_cause = PyObject_CallObject(cause, NULL);
+ if (fixed_cause == NULL)
+ goto bad;
+ } else if (PyExceptionInstance_Check(cause)) {
+ fixed_cause = cause;
+ Py_INCREF(fixed_cause);
+ } else {
+ PyErr_SetString(PyExc_TypeError,
+ "exception causes must derive from "
+ "BaseException");
+ goto bad;
+ }
+ PyException_SetCause(value, fixed_cause);
+ }
+ PyErr_SetObject(type, value);
+ if (tb) {
+#if CYTHON_COMPILING_IN_PYPY
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyErr_Fetch(tmp_type, tmp_value, tmp_tb);
+ Py_INCREF(tb);
+ PyErr_Restore(tmp_type, tmp_value, tb);
+ Py_XDECREF(tmp_tb);
+#else
+ PyThreadState *tstate = PyThreadState_GET();
+ PyObject* tmp_tb = tstate->curexc_traceback;
+ if (tb != tmp_tb) {
+ Py_INCREF(tb);
+ tstate->curexc_traceback = tb;
+ Py_XDECREF(tmp_tb);
+ }
+#endif
+ }
+bad:
+ Py_XDECREF(owned_instance);
+ return;
+}
+#endif
+
+static CYTHON_INLINE void __Pyx_RaiseNoneNotIterableError(void) {
+ PyErr_SetString(PyExc_TypeError, "'NoneType' object is not iterable");
+}
+
+static CYTHON_INLINE int __Pyx_TypeTest(PyObject *obj, PyTypeObject *type) {
+ if (unlikely(!type)) {
+ PyErr_SetString(PyExc_SystemError, "Missing type object");
+ return 0;
+ }
+ if (likely(PyObject_TypeCheck(obj, type)))
+ return 1;
+ PyErr_Format(PyExc_TypeError, "Cannot convert %.200s to %.200s",
+ Py_TYPE(obj)->tp_name, type->tp_name);
+ return 0;
+}
+
+static void __Pyx_RaiseDoubleKeywordsError(
+ const char* func_name,
+ PyObject* kw_name)
+{
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION >= 3
+ "%s() got multiple values for keyword argument '%U'", func_name, kw_name);
+ #else
+ "%s() got multiple values for keyword argument '%s'", func_name,
+ PyString_AsString(kw_name));
+ #endif
+}
+
+static int __Pyx_ParseOptionalKeywords(
+ PyObject *kwds,
+ PyObject **argnames[],
+ PyObject *kwds2,
+ PyObject *values[],
+ Py_ssize_t num_pos_args,
+ const char* function_name)
+{
+ PyObject *key = 0, *value = 0;
+ Py_ssize_t pos = 0;
+ PyObject*** name;
+ PyObject*** first_kw_arg = argnames + num_pos_args;
+ while (PyDict_Next(kwds, &pos, &key, &value)) {
+ name = first_kw_arg;
+ while (*name && (**name != key)) name++;
+ if (*name) {
+ values[name-argnames] = value;
+ continue;
+ }
+ name = first_kw_arg;
+ #if PY_MAJOR_VERSION < 3
+ if (likely(PyString_CheckExact(key)) || likely(PyString_Check(key))) {
+ while (*name) {
+ if ((CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**name) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**name, key)) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ if ((**argname == key) || (
+ (CYTHON_COMPILING_IN_PYPY || PyString_GET_SIZE(**argname) == PyString_GET_SIZE(key))
+ && _PyString_Eq(**argname, key))) {
+ goto arg_passed_twice;
+ }
+ argname++;
+ }
+ }
+ } else
+ #endif
+ if (likely(PyUnicode_Check(key))) {
+ while (*name) {
+ int cmp = (**name == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**name) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**name, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) {
+ values[name-argnames] = value;
+ break;
+ }
+ name++;
+ }
+ if (*name) continue;
+ else {
+ PyObject*** argname = argnames;
+ while (argname != first_kw_arg) {
+ int cmp = (**argname == key) ? 0 :
+ #if !CYTHON_COMPILING_IN_PYPY && PY_MAJOR_VERSION >= 3
+ (PyUnicode_GET_SIZE(**argname) != PyUnicode_GET_SIZE(key)) ? 1 :
+ #endif
+ PyUnicode_Compare(**argname, key);
+ if (cmp < 0 && unlikely(PyErr_Occurred())) goto bad;
+ if (cmp == 0) goto arg_passed_twice;
+ argname++;
+ }
+ }
+ } else
+ goto invalid_keyword_type;
+ if (kwds2) {
+ if (unlikely(PyDict_SetItem(kwds2, key, value))) goto bad;
+ } else {
+ goto invalid_keyword;
+ }
+ }
+ return 0;
+arg_passed_twice:
+ __Pyx_RaiseDoubleKeywordsError(function_name, key);
+ goto bad;
+invalid_keyword_type:
+ PyErr_Format(PyExc_TypeError,
+ "%.200s() keywords must be strings", function_name);
+ goto bad;
+invalid_keyword:
+ PyErr_Format(PyExc_TypeError,
+ #if PY_MAJOR_VERSION < 3
+ "%.200s() got an unexpected keyword argument '%.200s'",
+ function_name, PyString_AsString(key));
+ #else
+ "%s() got an unexpected keyword argument '%U'",
+ function_name, key);
+ #endif
+bad:
+ return -1;
+}
+
+static void __Pyx_RaiseArgumentTypeInvalid(const char* name, PyObject *obj, PyTypeObject *type) {
+ PyErr_Format(PyExc_TypeError,
+ "Argument '%.200s' has incorrect type (expected %.200s, got %.200s)",
+ name, type->tp_name, Py_TYPE(obj)->tp_name);
+}
+static CYTHON_INLINE int __Pyx_ArgTypeTest(PyObject *obj, PyTypeObject *type, int none_allowed,
+ const char *name, int exact)
+{
+ if (unlikely(!type)) {
+ PyErr_SetString(PyExc_SystemError, "Missing type object");
+ return 0;
+ }
+ if (none_allowed && obj == Py_None) return 1;
+ else if (exact) {
+ if (likely(Py_TYPE(obj) == type)) return 1;
+ #if PY_MAJOR_VERSION == 2
+ else if ((type == &PyBaseString_Type) && likely(__Pyx_PyBaseString_CheckExact(obj))) return 1;
+ #endif
+ }
+ else {
+ if (likely(PyObject_TypeCheck(obj, type))) return 1;
+ }
+ __Pyx_RaiseArgumentTypeInvalid(name, obj, type);
+ return 0;
+}
+
+static CYTHON_INLINE int __Pyx_PyBytes_Equals(PyObject* s1, PyObject* s2, int equals) {
+#if CYTHON_COMPILING_IN_PYPY
+ return PyObject_RichCompareBool(s1, s2, equals);
+#else
+ if (s1 == s2) {
+ return (equals == Py_EQ);
+ } else if (PyBytes_CheckExact(s1) & PyBytes_CheckExact(s2)) {
+ const char *ps1, *ps2;
+ Py_ssize_t length = PyBytes_GET_SIZE(s1);
+ if (length != PyBytes_GET_SIZE(s2))
+ return (equals == Py_NE);
+ ps1 = PyBytes_AS_STRING(s1);
+ ps2 = PyBytes_AS_STRING(s2);
+ if (ps1[0] != ps2[0]) {
+ return (equals == Py_NE);
+ } else if (length == 1) {
+ return (equals == Py_EQ);
+ } else {
+ int result = memcmp(ps1, ps2, (size_t)length);
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & PyBytes_CheckExact(s2)) {
+ return (equals == Py_NE);
+ } else if ((s2 == Py_None) & PyBytes_CheckExact(s1)) {
+ return (equals == Py_NE);
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+#endif
+}
+
+static CYTHON_INLINE int __Pyx_PyUnicode_Equals(PyObject* s1, PyObject* s2, int equals) {
+#if CYTHON_COMPILING_IN_PYPY
+ return PyObject_RichCompareBool(s1, s2, equals);
+#else
+#if PY_MAJOR_VERSION < 3
+ PyObject* owned_ref = NULL;
+#endif
+ int s1_is_unicode, s2_is_unicode;
+ if (s1 == s2) {
+ goto return_eq;
+ }
+ s1_is_unicode = PyUnicode_CheckExact(s1);
+ s2_is_unicode = PyUnicode_CheckExact(s2);
+#if PY_MAJOR_VERSION < 3
+ if ((s1_is_unicode & (!s2_is_unicode)) && PyString_CheckExact(s2)) {
+ owned_ref = PyUnicode_FromObject(s2);
+ if (unlikely(!owned_ref))
+ return -1;
+ s2 = owned_ref;
+ s2_is_unicode = 1;
+ } else if ((s2_is_unicode & (!s1_is_unicode)) && PyString_CheckExact(s1)) {
+ owned_ref = PyUnicode_FromObject(s1);
+ if (unlikely(!owned_ref))
+ return -1;
+ s1 = owned_ref;
+ s1_is_unicode = 1;
+ } else if (((!s2_is_unicode) & (!s1_is_unicode))) {
+ return __Pyx_PyBytes_Equals(s1, s2, equals);
+ }
+#endif
+ if (s1_is_unicode & s2_is_unicode) {
+ Py_ssize_t length;
+ int kind;
+ void *data1, *data2;
+ if (unlikely(__Pyx_PyUnicode_READY(s1) < 0) || unlikely(__Pyx_PyUnicode_READY(s2) < 0))
+ return -1;
+ length = __Pyx_PyUnicode_GET_LENGTH(s1);
+ if (length != __Pyx_PyUnicode_GET_LENGTH(s2)) {
+ goto return_ne;
+ }
+ kind = __Pyx_PyUnicode_KIND(s1);
+ if (kind != __Pyx_PyUnicode_KIND(s2)) {
+ goto return_ne;
+ }
+ data1 = __Pyx_PyUnicode_DATA(s1);
+ data2 = __Pyx_PyUnicode_DATA(s2);
+ if (__Pyx_PyUnicode_READ(kind, data1, 0) != __Pyx_PyUnicode_READ(kind, data2, 0)) {
+ goto return_ne;
+ } else if (length == 1) {
+ goto return_eq;
+ } else {
+ int result = memcmp(data1, data2, (size_t)(length * kind));
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(owned_ref);
+ #endif
+ return (equals == Py_EQ) ? (result == 0) : (result != 0);
+ }
+ } else if ((s1 == Py_None) & s2_is_unicode) {
+ goto return_ne;
+ } else if ((s2 == Py_None) & s1_is_unicode) {
+ goto return_ne;
+ } else {
+ int result;
+ PyObject* py_result = PyObject_RichCompare(s1, s2, equals);
+ if (!py_result)
+ return -1;
+ result = __Pyx_PyObject_IsTrue(py_result);
+ Py_DECREF(py_result);
+ return result;
+ }
+return_eq:
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(owned_ref);
+ #endif
+ return (equals == Py_EQ);
+return_ne:
+ #if PY_MAJOR_VERSION < 3
+ Py_XDECREF(owned_ref);
+ #endif
+ return (equals == Py_NE);
+#endif
+}
+
+static CYTHON_INLINE PyObject *__Pyx_GetAttr(PyObject *o, PyObject *n) {
+#if CYTHON_COMPILING_IN_CPYTHON
+#if PY_MAJOR_VERSION >= 3
+ if (likely(PyUnicode_Check(n)))
+#else
+ if (likely(PyString_Check(n)))
+#endif
+ return __Pyx_PyObject_GetAttrStr(o, n);
+#endif
+ return PyObject_GetAttr(o, n);
+}
+
+static CYTHON_INLINE PyObject* __Pyx_decode_c_string(
+ const char* cstring, Py_ssize_t start, Py_ssize_t stop,
+ const char* encoding, const char* errors,
+ PyObject* (*decode_func)(const char *s, Py_ssize_t size, const char *errors)) {
+ Py_ssize_t length;
+ if (unlikely((start < 0) | (stop < 0))) {
+ length = strlen(cstring);
+ if (start < 0) {
+ start += length;
+ if (start < 0)
+ start = 0;
+ }
+ if (stop < 0)
+ stop += length;
+ }
+ length = stop - start;
+ if (unlikely(length <= 0))
+ return PyUnicode_FromUnicode(NULL, 0);
+ cstring += start;
+ if (decode_func) {
+ return decode_func(cstring, length, errors);
+ } else {
+ return PyUnicode_Decode(cstring, length, encoding, errors);
+ }
+}
+
+static CYTHON_INLINE void __Pyx_ExceptionSave(PyObject **type, PyObject **value, PyObject **tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ *type = tstate->exc_type;
+ *value = tstate->exc_value;
+ *tb = tstate->exc_traceback;
+ Py_XINCREF(*type);
+ Py_XINCREF(*value);
+ Py_XINCREF(*tb);
+#else
+ PyErr_GetExcInfo(type, value, tb);
+#endif
+}
+static void __Pyx_ExceptionReset(PyObject *type, PyObject *value, PyObject *tb) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = type;
+ tstate->exc_value = value;
+ tstate->exc_traceback = tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(type, value, tb);
+#endif
+}
+
+static int __Pyx_GetException(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *local_type, *local_value, *local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+ PyThreadState *tstate = PyThreadState_GET();
+ local_type = tstate->curexc_type;
+ local_value = tstate->curexc_value;
+ local_tb = tstate->curexc_traceback;
+ tstate->curexc_type = 0;
+ tstate->curexc_value = 0;
+ tstate->curexc_traceback = 0;
+#else
+ PyErr_Fetch(&local_type, &local_value, &local_tb);
+#endif
+ PyErr_NormalizeException(&local_type, &local_value, &local_tb);
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (unlikely(tstate->curexc_type))
+#else
+ if (unlikely(PyErr_Occurred()))
+#endif
+ goto bad;
+ #if PY_MAJOR_VERSION >= 3
+ if (local_tb) {
+ if (unlikely(PyException_SetTraceback(local_value, local_tb) < 0))
+ goto bad;
+ }
+ #endif
+ Py_XINCREF(local_tb);
+ Py_XINCREF(local_type);
+ Py_XINCREF(local_value);
+ *type = local_type;
+ *value = local_value;
+ *tb = local_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = local_type;
+ tstate->exc_value = local_value;
+ tstate->exc_traceback = local_tb;
+ Py_XDECREF(tmp_type);
+ Py_XDECREF(tmp_value);
+ Py_XDECREF(tmp_tb);
+#else
+ PyErr_SetExcInfo(local_type, local_value, local_tb);
+#endif
+ return 0;
+bad:
+ *type = 0;
+ *value = 0;
+ *tb = 0;
+ Py_XDECREF(local_type);
+ Py_XDECREF(local_value);
+ Py_XDECREF(local_tb);
+ return -1;
+}
+
+static CYTHON_INLINE void __Pyx_ExceptionSwap(PyObject **type, PyObject **value, PyObject **tb) {
+ PyObject *tmp_type, *tmp_value, *tmp_tb;
+#if CYTHON_COMPILING_IN_CPYTHON
+ PyThreadState *tstate = PyThreadState_GET();
+ tmp_type = tstate->exc_type;
+ tmp_value = tstate->exc_value;
+ tmp_tb = tstate->exc_traceback;
+ tstate->exc_type = *type;
+ tstate->exc_value = *value;
+ tstate->exc_traceback = *tb;
+#else
+ PyErr_GetExcInfo(&tmp_type, &tmp_value, &tmp_tb);
+ PyErr_SetExcInfo(*type, *value, *tb);
+#endif
+ *type = tmp_type;
+ *value = tmp_value;
+ *tb = tmp_tb;
+}
+
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Generic(PyObject *o, PyObject* j) {
+ PyObject *r;
+ if (!j) return NULL;
+ r = PyObject_GetItem(o, j);
+ Py_DECREF(j);
+ return r;
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_List_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (wraparound & unlikely(i < 0)) i += PyList_GET_SIZE(o);
+ if ((!boundscheck) || likely((0 <= i) & (i < PyList_GET_SIZE(o)))) {
+ PyObject *r = PyList_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Tuple_Fast(PyObject *o, Py_ssize_t i,
+ int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (wraparound & unlikely(i < 0)) i += PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((0 <= i) & (i < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, i);
+ Py_INCREF(r);
+ return r;
+ }
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+#else
+ return PySequence_GetItem(o, i);
+#endif
+}
+static CYTHON_INLINE PyObject *__Pyx_GetItemInt_Fast(PyObject *o, Py_ssize_t i,
+ int is_list, int wraparound, int boundscheck) {
+#if CYTHON_COMPILING_IN_CPYTHON
+ if (is_list || PyList_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyList_GET_SIZE(o);
+ if ((!boundscheck) || (likely((n >= 0) & (n < PyList_GET_SIZE(o))))) {
+ PyObject *r = PyList_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ }
+ else if (PyTuple_CheckExact(o)) {
+ Py_ssize_t n = ((!wraparound) | likely(i >= 0)) ? i : i + PyTuple_GET_SIZE(o);
+ if ((!boundscheck) || likely((n >= 0) & (n < PyTuple_GET_SIZE(o)))) {
+ PyObject *r = PyTuple_GET_ITEM(o, n);
+ Py_INCREF(r);
+ return r;
+ }
+ } else {
+ PySequenceMethods *m = Py_TYPE(o)->tp_as_sequence;
+ if (likely(m && m->sq_item)) {
+ if (wraparound && unlikely(i < 0) && likely(m->sq_length)) {
+ Py_ssize_t l = m->sq_length(o);
+ if (likely(l >= 0)) {
+ i += l;
+ } else {
+ if (PyErr_ExceptionMatches(PyExc_OverflowError))
+ PyErr_Clear();
+ else
+ return NULL;
+ }
+ }
+ return m->sq_item(o, i);
+ }
+ }
+#else
+ if (is_list || PySequence_Check(o)) {
+ return PySequence_GetItem(o, i);
+ }
+#endif
+ return __Pyx_GetItemInt_Generic(o, PyInt_FromSsize_t(i));
+}
+
+static CYTHON_INLINE void __Pyx_RaiseUnboundLocalError(const char *varname) {
+ PyErr_Format(PyExc_UnboundLocalError, "local variable '%s' referenced before assignment", varname);
+}
+
+static void __Pyx_WriteUnraisable(const char *name, CYTHON_UNUSED int clineno,
+ CYTHON_UNUSED int lineno, CYTHON_UNUSED const char *filename,
+ int full_traceback) {
+ PyObject *old_exc, *old_val, *old_tb;
+ PyObject *ctx;
+ __Pyx_ErrFetch(&old_exc, &old_val, &old_tb);
+ if (full_traceback) {
+ Py_XINCREF(old_exc);
+ Py_XINCREF(old_val);
+ Py_XINCREF(old_tb);
+ __Pyx_ErrRestore(old_exc, old_val, old_tb);
+ PyErr_PrintEx(1);
+ }
+ #if PY_MAJOR_VERSION < 3
+ ctx = PyString_FromString(name);
+ #else
+ ctx = PyUnicode_FromString(name);
+ #endif
+ __Pyx_ErrRestore(old_exc, old_val, old_tb);
+ if (!ctx) {
+ PyErr_WriteUnraisable(Py_None);
+ } else {
+ PyErr_WriteUnraisable(ctx);
+ Py_DECREF(ctx);
+ }
+}
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallMethO(PyObject *func, PyObject *arg) {
+ PyObject *self, *result;
+ PyCFunction cfunc;
+ cfunc = PyCFunction_GET_FUNCTION(func);
+ self = PyCFunction_GET_SELF(func);
+ if (unlikely(Py_EnterRecursiveCall((char*)" while calling a Python object")))
+ return NULL;
+ result = cfunc(self, arg);
+ Py_LeaveRecursiveCall();
+ if (unlikely(!result) && unlikely(!PyErr_Occurred())) {
+ PyErr_SetString(
+ PyExc_SystemError,
+ "NULL result without error in PyObject_Call");
+ }
+ return result;
+}
+#endif
+
+#if CYTHON_COMPILING_IN_CPYTHON
+static PyObject* __Pyx__PyObject_CallOneArg(PyObject *func, PyObject *arg) {
+ PyObject *result;
+ PyObject *args = PyTuple_New(1);
+ if (unlikely(!args)) return NULL;
+ Py_INCREF(arg);
+ PyTuple_SET_ITEM(args, 0, arg);
+ result = __Pyx_PyObject_Call(func, args, NULL);
+ Py_DECREF(args);
+ return result;
+}
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
+#ifdef __Pyx_CyFunction_USED
+ if (likely(PyCFunction_Check(func) || PyObject_TypeCheck(func, __pyx_CyFunctionType))) {
+#else
+ if (likely(PyCFunction_Check(func))) {
+#endif
+ if (likely(PyCFunction_GET_FLAGS(func) & METH_O)) {
+ return __Pyx_PyObject_CallMethO(func, arg);
+ }
+ }
+ return __Pyx__PyObject_CallOneArg(func, arg);
+}
+#else
+static CYTHON_INLINE PyObject* __Pyx_PyObject_CallOneArg(PyObject *func, PyObject *arg) {
+ PyObject* args = PyTuple_Pack(1, arg);
+ return (likely(args)) ? __Pyx_PyObject_Call(func, args, NULL) : NULL;
+}
+#endif
+
+static int __Pyx_SetVtable(PyObject *dict, void *vtable) {
+#if PY_VERSION_HEX >= 0x02070000
+ PyObject *ob = PyCapsule_New(vtable, 0, 0);
+#else
+ PyObject *ob = PyCObject_FromVoidPtr(vtable, 0);
+#endif
+ if (!ob)
+ goto bad;
+ if (PyDict_SetItem(dict, __pyx_n_s_pyx_vtable, ob) < 0)
+ goto bad;
+ Py_DECREF(ob);
+ return 0;
+bad:
+ Py_XDECREF(ob);
+ return -1;
+}
+
+static int __pyx_bisect_code_objects(__Pyx_CodeObjectCacheEntry* entries, int count, int code_line) {
+ int start = 0, mid = 0, end = count - 1;
+ if (end >= 0 && code_line > entries[end].code_line) {
+ return count;
+ }
+ while (start < end) {
+ mid = (start + end) / 2;
+ if (code_line < entries[mid].code_line) {
+ end = mid;
+ } else if (code_line > entries[mid].code_line) {
+ start = mid + 1;
+ } else {
+ return mid;
+ }
+ }
+ if (code_line <= entries[mid].code_line) {
+ return mid;
+ } else {
+ return mid + 1;
+ }
+}
+static PyCodeObject *__pyx_find_code_object(int code_line) {
+ PyCodeObject* code_object;
+ int pos;
+ if (unlikely(!code_line) || unlikely(!__pyx_code_cache.entries)) {
+ return NULL;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if (unlikely(pos >= __pyx_code_cache.count) || unlikely(__pyx_code_cache.entries[pos].code_line != code_line)) {
+ return NULL;
+ }
+ code_object = __pyx_code_cache.entries[pos].code_object;
+ Py_INCREF(code_object);
+ return code_object;
+}
+static void __pyx_insert_code_object(int code_line, PyCodeObject* code_object) {
+ int pos, i;
+ __Pyx_CodeObjectCacheEntry* entries = __pyx_code_cache.entries;
+ if (unlikely(!code_line)) {
+ return;
+ }
+ if (unlikely(!entries)) {
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Malloc(64*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (likely(entries)) {
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = 64;
+ __pyx_code_cache.count = 1;
+ entries[0].code_line = code_line;
+ entries[0].code_object = code_object;
+ Py_INCREF(code_object);
+ }
+ return;
+ }
+ pos = __pyx_bisect_code_objects(__pyx_code_cache.entries, __pyx_code_cache.count, code_line);
+ if ((pos < __pyx_code_cache.count) && unlikely(__pyx_code_cache.entries[pos].code_line == code_line)) {
+ PyCodeObject* tmp = entries[pos].code_object;
+ entries[pos].code_object = code_object;
+ Py_DECREF(tmp);
+ return;
+ }
+ if (__pyx_code_cache.count == __pyx_code_cache.max_count) {
+ int new_max = __pyx_code_cache.max_count + 64;
+ entries = (__Pyx_CodeObjectCacheEntry*)PyMem_Realloc(
+ __pyx_code_cache.entries, (size_t)new_max*sizeof(__Pyx_CodeObjectCacheEntry));
+ if (unlikely(!entries)) {
+ return;
+ }
+ __pyx_code_cache.entries = entries;
+ __pyx_code_cache.max_count = new_max;
+ }
+ for (i=__pyx_code_cache.count; i>pos; i--) {
+ entries[i] = entries[i-1];
+ }
+ entries[pos].code_line = code_line;
+ entries[pos].code_object = code_object;
+ __pyx_code_cache.count++;
+ Py_INCREF(code_object);
+}
+
+#include "compile.h"
+#include "frameobject.h"
+#include "traceback.h"
+static PyCodeObject* __Pyx_CreateCodeObjectForTraceback(
+ const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyObject *py_srcfile = 0;
+ PyObject *py_funcname = 0;
+ #if PY_MAJOR_VERSION < 3
+ py_srcfile = PyString_FromString(filename);
+ #else
+ py_srcfile = PyUnicode_FromString(filename);
+ #endif
+ if (!py_srcfile) goto bad;
+ if (c_line) {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #else
+ py_funcname = PyUnicode_FromFormat( "%s (%s:%d)", funcname, __pyx_cfilenm, c_line);
+ #endif
+ }
+ else {
+ #if PY_MAJOR_VERSION < 3
+ py_funcname = PyString_FromString(funcname);
+ #else
+ py_funcname = PyUnicode_FromString(funcname);
+ #endif
+ }
+ if (!py_funcname) goto bad;
+ py_code = __Pyx_PyCode_New(
+ 0,
+ 0,
+ 0,
+ 0,
+ 0,
+ __pyx_empty_bytes, /*PyObject *code,*/
+ __pyx_empty_tuple, /*PyObject *consts,*/
+ __pyx_empty_tuple, /*PyObject *names,*/
+ __pyx_empty_tuple, /*PyObject *varnames,*/
+ __pyx_empty_tuple, /*PyObject *freevars,*/
+ __pyx_empty_tuple, /*PyObject *cellvars,*/
+ py_srcfile, /*PyObject *filename,*/
+ py_funcname, /*PyObject *name,*/
+ py_line,
+ __pyx_empty_bytes /*PyObject *lnotab*/
+ );
+ Py_DECREF(py_srcfile);
+ Py_DECREF(py_funcname);
+ return py_code;
+bad:
+ Py_XDECREF(py_srcfile);
+ Py_XDECREF(py_funcname);
+ return NULL;
+}
+static void __Pyx_AddTraceback(const char *funcname, int c_line,
+ int py_line, const char *filename) {
+ PyCodeObject *py_code = 0;
+ PyFrameObject *py_frame = 0;
+ py_code = __pyx_find_code_object(c_line ? c_line : py_line);
+ if (!py_code) {
+ py_code = __Pyx_CreateCodeObjectForTraceback(
+ funcname, c_line, py_line, filename);
+ if (!py_code) goto bad;
+ __pyx_insert_code_object(c_line ? c_line : py_line, py_code);
+ }
+ py_frame = PyFrame_New(
+ PyThreadState_GET(), /*PyThreadState *tstate,*/
+ py_code, /*PyCodeObject *code,*/
+ __pyx_d, /*PyObject *globals,*/
+ 0 /*PyObject *locals*/
+ );
+ if (!py_frame) goto bad;
+ py_frame->f_lineno = py_line;
+ PyTraceBack_Here(py_frame);
+bad:
+ Py_XDECREF(py_code);
+ Py_XDECREF(py_frame);
+}
+
+#if PY_MAJOR_VERSION < 3
+static int __Pyx_GetBuffer(PyObject *obj, Py_buffer *view, int flags) {
+ if (PyObject_CheckBuffer(obj)) return PyObject_GetBuffer(obj, view, flags);
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) return __pyx_pw_5numpy_7ndarray_1__getbuffer__(obj, view, flags);
+ if (PyObject_TypeCheck(obj, __pyx_array_type)) return __pyx_array_getbuffer(obj, view, flags);
+ if (PyObject_TypeCheck(obj, __pyx_memoryview_type)) return __pyx_memoryview_getbuffer(obj, view, flags);
+ PyErr_Format(PyExc_TypeError, "'%.200s' does not have the buffer interface", Py_TYPE(obj)->tp_name);
+ return -1;
+}
+static void __Pyx_ReleaseBuffer(Py_buffer *view) {
+ PyObject *obj = view->obj;
+ if (!obj) return;
+ if (PyObject_CheckBuffer(obj)) {
+ PyBuffer_Release(view);
+ return;
+ }
+ if (PyObject_TypeCheck(obj, __pyx_ptype_5numpy_ndarray)) { __pyx_pw_5numpy_7ndarray_3__releasebuffer__(obj, view); return; }
+ Py_DECREF(obj);
+ view->obj = NULL;
+}
+#endif
+
+
+ static PyObject *__Pyx_Import(PyObject *name, PyObject *from_list, int level) {
+ PyObject *empty_list = 0;
+ PyObject *module = 0;
+ PyObject *global_dict = 0;
+ PyObject *empty_dict = 0;
+ PyObject *list;
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_import;
+ py_import = __Pyx_PyObject_GetAttrStr(__pyx_b, __pyx_n_s_import);
+ if (!py_import)
+ goto bad;
+ #endif
+ if (from_list)
+ list = from_list;
+ else {
+ empty_list = PyList_New(0);
+ if (!empty_list)
+ goto bad;
+ list = empty_list;
+ }
+ global_dict = PyModule_GetDict(__pyx_m);
+ if (!global_dict)
+ goto bad;
+ empty_dict = PyDict_New();
+ if (!empty_dict)
+ goto bad;
+ {
+ #if PY_MAJOR_VERSION >= 3
+ if (level == -1) {
+ if (strchr(__Pyx_MODULE_NAME, '.')) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(1);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, 1);
+ #endif
+ if (!module) {
+ if (!PyErr_ExceptionMatches(PyExc_ImportError))
+ goto bad;
+ PyErr_Clear();
+ }
+ }
+ level = 0;
+ }
+ #endif
+ if (!module) {
+ #if PY_VERSION_HEX < 0x03030000
+ PyObject *py_level = PyInt_FromLong(level);
+ if (!py_level)
+ goto bad;
+ module = PyObject_CallFunctionObjArgs(py_import,
+ name, global_dict, empty_dict, list, py_level, NULL);
+ Py_DECREF(py_level);
+ #else
+ module = PyImport_ImportModuleLevelObject(
+ name, global_dict, empty_dict, list, level);
+ #endif
+ }
+ }
+bad:
+ #if PY_VERSION_HEX < 0x03030000
+ Py_XDECREF(py_import);
+ #endif
+ Py_XDECREF(empty_list);
+ Py_XDECREF(empty_dict);
+ return module;
+}
+
+#define __PYX_VERIFY_RETURN_INT(target_type, func_type, func_value) \
+ { \
+ func_type value = func_value; \
+ if (sizeof(target_type) < sizeof(func_type)) { \
+ if (unlikely(value != (func_type) (target_type) value)) { \
+ func_type zero = 0; \
+ if (is_unsigned && unlikely(value < zero)) \
+ goto raise_neg_overflow; \
+ else \
+ goto raise_overflow; \
+ } \
+ } \
+ return (target_type) value; \
+ }
+
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ #include "longintrepr.h"
+ #endif
+#endif
+
+static CYTHON_INLINE size_t __Pyx_PyInt_As_size_t(PyObject *x) {
+ const size_t neg_one = (size_t) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(size_t) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(size_t, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (size_t) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+ if (sizeof(size_t) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT(size_t, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(size_t) <= sizeof(unsigned long long)) {
+ __PYX_VERIFY_RETURN_INT(size_t, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ }
+ } else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(size_t, digit, +(((PyLongObject*)x)->ob_digit[0]));
+ case -1: __PYX_VERIFY_RETURN_INT(size_t, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (sizeof(size_t) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(size_t, long, PyLong_AsLong(x))
+ } else if (sizeof(size_t) <= sizeof(long long)) {
+ __PYX_VERIFY_RETURN_INT(size_t, long long, PyLong_AsLongLong(x))
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ size_t val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (size_t) -1;
+ }
+ } else {
+ size_t val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (size_t) -1;
+ val = __Pyx_PyInt_As_size_t(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to size_t");
+ return (size_t) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to size_t");
+ return (size_t) -1;
+}
+
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
+ return ::std::complex< float >(x, y);
+ }
+ #else
+ static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
+ return x + y*(__pyx_t_float_complex)_Complex_I;
+ }
+ #endif
+#else
+ static CYTHON_INLINE __pyx_t_float_complex __pyx_t_float_complex_from_parts(float x, float y) {
+ __pyx_t_float_complex z;
+ z.real = x;
+ z.imag = y;
+ return z;
+ }
+#endif
+
+#if CYTHON_CCOMPLEX
+#else
+ static CYTHON_INLINE int __Pyx_c_eqf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ return (a.real == b.real) && (a.imag == b.imag);
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_sumf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ z.real = a.real + b.real;
+ z.imag = a.imag + b.imag;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_difff(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ z.real = a.real - b.real;
+ z.imag = a.imag - b.imag;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_prodf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ z.real = a.real * b.real - a.imag * b.imag;
+ z.imag = a.real * b.imag + a.imag * b.real;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_quotf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ float denom = b.real * b.real + b.imag * b.imag;
+ z.real = (a.real * b.real + a.imag * b.imag) / denom;
+ z.imag = (a.imag * b.real - a.real * b.imag) / denom;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_negf(__pyx_t_float_complex a) {
+ __pyx_t_float_complex z;
+ z.real = -a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+ static CYTHON_INLINE int __Pyx_c_is_zerof(__pyx_t_float_complex a) {
+ return (a.real == 0) && (a.imag == 0);
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_conjf(__pyx_t_float_complex a) {
+ __pyx_t_float_complex z;
+ z.real = a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+ #if 1
+ static CYTHON_INLINE float __Pyx_c_absf(__pyx_t_float_complex z) {
+ #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
+ return sqrtf(z.real*z.real + z.imag*z.imag);
+ #else
+ return hypotf(z.real, z.imag);
+ #endif
+ }
+ static CYTHON_INLINE __pyx_t_float_complex __Pyx_c_powf(__pyx_t_float_complex a, __pyx_t_float_complex b) {
+ __pyx_t_float_complex z;
+ float r, lnr, theta, z_r, z_theta;
+ if (b.imag == 0 && b.real == (int)b.real) {
+ if (b.real < 0) {
+ float denom = a.real * a.real + a.imag * a.imag;
+ a.real = a.real / denom;
+ a.imag = -a.imag / denom;
+ b.real = -b.real;
+ }
+ switch ((int)b.real) {
+ case 0:
+ z.real = 1;
+ z.imag = 0;
+ return z;
+ case 1:
+ return a;
+ case 2:
+ z = __Pyx_c_prodf(a, a);
+ return __Pyx_c_prodf(a, a);
+ case 3:
+ z = __Pyx_c_prodf(a, a);
+ return __Pyx_c_prodf(z, a);
+ case 4:
+ z = __Pyx_c_prodf(a, a);
+ return __Pyx_c_prodf(z, z);
+ }
+ }
+ if (a.imag == 0) {
+ if (a.real == 0) {
+ return a;
+ }
+ r = a.real;
+ theta = 0;
+ } else {
+ r = __Pyx_c_absf(a);
+ theta = atan2f(a.imag, a.real);
+ }
+ lnr = logf(r);
+ z_r = expf(lnr * b.real - theta * b.imag);
+ z_theta = theta * b.real + lnr * b.imag;
+ z.real = z_r * cosf(z_theta);
+ z.imag = z_r * sinf(z_theta);
+ return z;
+ }
+ #endif
+#endif
+
+#if CYTHON_CCOMPLEX
+ #ifdef __cplusplus
+ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
+ return ::std::complex< double >(x, y);
+ }
+ #else
+ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
+ return x + y*(__pyx_t_double_complex)_Complex_I;
+ }
+ #endif
+#else
+ static CYTHON_INLINE __pyx_t_double_complex __pyx_t_double_complex_from_parts(double x, double y) {
+ __pyx_t_double_complex z;
+ z.real = x;
+ z.imag = y;
+ return z;
+ }
+#endif
+
+#if CYTHON_CCOMPLEX
+#else
+ static CYTHON_INLINE int __Pyx_c_eq(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ return (a.real == b.real) && (a.imag == b.imag);
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_sum(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ z.real = a.real + b.real;
+ z.imag = a.imag + b.imag;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_diff(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ z.real = a.real - b.real;
+ z.imag = a.imag - b.imag;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_prod(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ z.real = a.real * b.real - a.imag * b.imag;
+ z.imag = a.real * b.imag + a.imag * b.real;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_quot(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ double denom = b.real * b.real + b.imag * b.imag;
+ z.real = (a.real * b.real + a.imag * b.imag) / denom;
+ z.imag = (a.imag * b.real - a.real * b.imag) / denom;
+ return z;
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_neg(__pyx_t_double_complex a) {
+ __pyx_t_double_complex z;
+ z.real = -a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+ static CYTHON_INLINE int __Pyx_c_is_zero(__pyx_t_double_complex a) {
+ return (a.real == 0) && (a.imag == 0);
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_conj(__pyx_t_double_complex a) {
+ __pyx_t_double_complex z;
+ z.real = a.real;
+ z.imag = -a.imag;
+ return z;
+ }
+ #if 1
+ static CYTHON_INLINE double __Pyx_c_abs(__pyx_t_double_complex z) {
+ #if !defined(HAVE_HYPOT) || defined(_MSC_VER)
+ return sqrt(z.real*z.real + z.imag*z.imag);
+ #else
+ return hypot(z.real, z.imag);
+ #endif
+ }
+ static CYTHON_INLINE __pyx_t_double_complex __Pyx_c_pow(__pyx_t_double_complex a, __pyx_t_double_complex b) {
+ __pyx_t_double_complex z;
+ double r, lnr, theta, z_r, z_theta;
+ if (b.imag == 0 && b.real == (int)b.real) {
+ if (b.real < 0) {
+ double denom = a.real * a.real + a.imag * a.imag;
+ a.real = a.real / denom;
+ a.imag = -a.imag / denom;
+ b.real = -b.real;
+ }
+ switch ((int)b.real) {
+ case 0:
+ z.real = 1;
+ z.imag = 0;
+ return z;
+ case 1:
+ return a;
+ case 2:
+ z = __Pyx_c_prod(a, a);
+ return __Pyx_c_prod(a, a);
+ case 3:
+ z = __Pyx_c_prod(a, a);
+ return __Pyx_c_prod(z, a);
+ case 4:
+ z = __Pyx_c_prod(a, a);
+ return __Pyx_c_prod(z, z);
+ }
+ }
+ if (a.imag == 0) {
+ if (a.real == 0) {
+ return a;
+ }
+ r = a.real;
+ theta = 0;
+ } else {
+ r = __Pyx_c_abs(a);
+ theta = atan2(a.imag, a.real);
+ }
+ lnr = log(r);
+ z_r = exp(lnr * b.real - theta * b.imag);
+ z_theta = theta * b.real + lnr * b.imag;
+ z.real = z_r * cos(z_theta);
+ z.imag = z_r * sin(z_theta);
+ return z;
+ }
+ #endif
+#endif
+
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_int(int value) {
+ const int neg_one = (int) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(int) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(int) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(int) <= sizeof(unsigned long long)) {
+ return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ }
+ } else {
+ if (sizeof(int) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(int) <= sizeof(long long)) {
+ return PyLong_FromLongLong((long long) value);
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(int),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE int __Pyx_PyInt_As_int(PyObject *x) {
+ const int neg_one = (int) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(int) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(int, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (int) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(int, digit, ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+ if (sizeof(int) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(int) <= sizeof(unsigned long long)) {
+ __PYX_VERIFY_RETURN_INT(int, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ }
+ } else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(int, digit, +(((PyLongObject*)x)->ob_digit[0]));
+ case -1: __PYX_VERIFY_RETURN_INT(int, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (sizeof(int) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(int, long, PyLong_AsLong(x))
+ } else if (sizeof(int) <= sizeof(long long)) {
+ __PYX_VERIFY_RETURN_INT(int, long long, PyLong_AsLongLong(x))
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ int val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (int) -1;
+ }
+ } else {
+ int val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (int) -1;
+ val = __Pyx_PyInt_As_int(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to int");
+ return (int) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to int");
+ return (int) -1;
+}
+
+static int
+__pyx_memviewslice_is_contig(const __Pyx_memviewslice *mvs,
+ char order, int ndim)
+{
+ int i, index, step, start;
+ Py_ssize_t itemsize = mvs->memview->view.itemsize;
+ if (order == 'F') {
+ step = 1;
+ start = 0;
+ } else {
+ step = -1;
+ start = ndim - 1;
+ }
+ for (i = 0; i < ndim; i++) {
+ index = start + step * i;
+ if (mvs->suboffsets[index] >= 0 || mvs->strides[index] != itemsize)
+ return 0;
+ itemsize *= mvs->shape[index];
+ }
+ return 1;
+}
+
+static void
+__pyx_get_array_memory_extents(__Pyx_memviewslice *slice,
+ void **out_start, void **out_end,
+ int ndim, size_t itemsize)
+{
+ char *start, *end;
+ int i;
+ start = end = slice->data;
+ for (i = 0; i < ndim; i++) {
+ Py_ssize_t stride = slice->strides[i];
+ Py_ssize_t extent = slice->shape[i];
+ if (extent == 0) {
+ *out_start = *out_end = start;
+ return;
+ } else {
+ if (stride > 0)
+ end += stride * (extent - 1);
+ else
+ start += stride * (extent - 1);
+ }
+ }
+ *out_start = start;
+ *out_end = end + itemsize;
+}
+static int
+__pyx_slices_overlap(__Pyx_memviewslice *slice1,
+ __Pyx_memviewslice *slice2,
+ int ndim, size_t itemsize)
+{
+ void *start1, *end1, *start2, *end2;
+ __pyx_get_array_memory_extents(slice1, &start1, &end1, ndim, itemsize);
+ __pyx_get_array_memory_extents(slice2, &start2, &end2, ndim, itemsize);
+ return (start1 < end2) && (start2 < end1);
+}
+
+static __Pyx_memviewslice
+__pyx_memoryview_copy_new_contig(const __Pyx_memviewslice *from_mvs,
+ const char *mode, int ndim,
+ size_t sizeof_dtype, int contig_flag,
+ int dtype_is_object)
+{
+ __Pyx_RefNannyDeclarations
+ int i;
+ __Pyx_memviewslice new_mvs = { 0, 0, { 0 }, { 0 }, { 0 } };
+ struct __pyx_memoryview_obj *from_memview = from_mvs->memview;
+ Py_buffer *buf = &from_memview->view;
+ PyObject *shape_tuple = NULL;
+ PyObject *temp_int = NULL;
+ struct __pyx_array_obj *array_obj = NULL;
+ struct __pyx_memoryview_obj *memview_obj = NULL;
+ __Pyx_RefNannySetupContext("__pyx_memoryview_copy_new_contig", 0);
+ for (i = 0; i < ndim; i++) {
+ if (from_mvs->suboffsets[i] >= 0) {
+ PyErr_Format(PyExc_ValueError, "Cannot copy memoryview slice with "
+ "indirect dimensions (axis %d)", i);
+ goto fail;
+ }
+ }
+ shape_tuple = PyTuple_New(ndim);
+ if (unlikely(!shape_tuple)) {
+ goto fail;
+ }
+ __Pyx_GOTREF(shape_tuple);
+ for(i = 0; i < ndim; i++) {
+ temp_int = PyInt_FromSsize_t(from_mvs->shape[i]);
+ if(unlikely(!temp_int)) {
+ goto fail;
+ } else {
+ PyTuple_SET_ITEM(shape_tuple, i, temp_int);
+ temp_int = NULL;
+ }
+ }
+ array_obj = __pyx_array_new(shape_tuple, sizeof_dtype, buf->format, (char *) mode, NULL);
+ if (unlikely(!array_obj)) {
+ goto fail;
+ }
+ __Pyx_GOTREF(array_obj);
+ memview_obj = (struct __pyx_memoryview_obj *) __pyx_memoryview_new(
+ (PyObject *) array_obj, contig_flag,
+ dtype_is_object,
+ from_mvs->memview->typeinfo);
+ if (unlikely(!memview_obj))
+ goto fail;
+ if (unlikely(__Pyx_init_memviewslice(memview_obj, ndim, &new_mvs, 1) < 0))
+ goto fail;
+ if (unlikely(__pyx_memoryview_copy_contents(*from_mvs, new_mvs, ndim, ndim,
+ dtype_is_object) < 0))
+ goto fail;
+ goto no_fail;
+fail:
+ __Pyx_XDECREF(new_mvs.memview);
+ new_mvs.memview = NULL;
+ new_mvs.data = NULL;
+no_fail:
+ __Pyx_XDECREF(shape_tuple);
+ __Pyx_XDECREF(temp_int);
+ __Pyx_XDECREF(array_obj);
+ __Pyx_RefNannyFinishContext();
+ return new_mvs;
+}
+
+static CYTHON_INLINE PyObject *
+__pyx_capsule_create(void *p, CYTHON_UNUSED const char *sig)
+{
+ PyObject *cobj;
+#if PY_VERSION_HEX >= 0x02070000
+ cobj = PyCapsule_New(p, sig, NULL);
+#else
+ cobj = PyCObject_FromVoidPtr(p, NULL);
+#endif
+ return cobj;
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyInt_From_long(long value) {
+ const long neg_one = (long) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+ if (is_unsigned) {
+ if (sizeof(long) < sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(long) <= sizeof(unsigned long)) {
+ return PyLong_FromUnsignedLong((unsigned long) value);
+ } else if (sizeof(long) <= sizeof(unsigned long long)) {
+ return PyLong_FromUnsignedLongLong((unsigned long long) value);
+ }
+ } else {
+ if (sizeof(long) <= sizeof(long)) {
+ return PyInt_FromLong((long) value);
+ } else if (sizeof(long) <= sizeof(long long)) {
+ return PyLong_FromLongLong((long long) value);
+ }
+ }
+ {
+ int one = 1; int little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&value;
+ return _PyLong_FromByteArray(bytes, sizeof(long),
+ little, !is_unsigned);
+ }
+}
+
+static CYTHON_INLINE char __Pyx_PyInt_As_char(PyObject *x) {
+ const char neg_one = (char) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(char) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(char, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (char) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(char, digit, ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+ if (sizeof(char) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT(char, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(char) <= sizeof(unsigned long long)) {
+ __PYX_VERIFY_RETURN_INT(char, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ }
+ } else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(char, digit, +(((PyLongObject*)x)->ob_digit[0]));
+ case -1: __PYX_VERIFY_RETURN_INT(char, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (sizeof(char) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(char, long, PyLong_AsLong(x))
+ } else if (sizeof(char) <= sizeof(long long)) {
+ __PYX_VERIFY_RETURN_INT(char, long long, PyLong_AsLongLong(x))
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ char val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (char) -1;
+ }
+ } else {
+ char val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (char) -1;
+ val = __Pyx_PyInt_As_char(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to char");
+ return (char) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to char");
+ return (char) -1;
+}
+
+static CYTHON_INLINE long __Pyx_PyInt_As_long(PyObject *x) {
+ const long neg_one = (long) -1, const_zero = 0;
+ const int is_unsigned = neg_one > const_zero;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_Check(x))) {
+ if (sizeof(long) < sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(long, long, PyInt_AS_LONG(x))
+ } else {
+ long val = PyInt_AS_LONG(x);
+ if (is_unsigned && unlikely(val < 0)) {
+ goto raise_neg_overflow;
+ }
+ return (long) val;
+ }
+ } else
+#endif
+ if (likely(PyLong_Check(x))) {
+ if (is_unsigned) {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(long, digit, ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (unlikely(Py_SIZE(x) < 0)) {
+ goto raise_neg_overflow;
+ }
+ if (sizeof(long) <= sizeof(unsigned long)) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long, PyLong_AsUnsignedLong(x))
+ } else if (sizeof(long) <= sizeof(unsigned long long)) {
+ __PYX_VERIFY_RETURN_INT(long, unsigned long long, PyLong_AsUnsignedLongLong(x))
+ }
+ } else {
+#if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(x)) {
+ case 0: return 0;
+ case 1: __PYX_VERIFY_RETURN_INT(long, digit, +(((PyLongObject*)x)->ob_digit[0]));
+ case -1: __PYX_VERIFY_RETURN_INT(long, sdigit, -(sdigit) ((PyLongObject*)x)->ob_digit[0]);
+ }
+ #endif
+#endif
+ if (sizeof(long) <= sizeof(long)) {
+ __PYX_VERIFY_RETURN_INT(long, long, PyLong_AsLong(x))
+ } else if (sizeof(long) <= sizeof(long long)) {
+ __PYX_VERIFY_RETURN_INT(long, long long, PyLong_AsLongLong(x))
+ }
+ }
+ {
+#if CYTHON_COMPILING_IN_PYPY && !defined(_PyLong_AsByteArray)
+ PyErr_SetString(PyExc_RuntimeError,
+ "_PyLong_AsByteArray() not available in PyPy, cannot convert large numbers");
+#else
+ long val;
+ PyObject *v = __Pyx_PyNumber_Int(x);
+ #if PY_MAJOR_VERSION < 3
+ if (likely(v) && !PyLong_Check(v)) {
+ PyObject *tmp = v;
+ v = PyNumber_Long(tmp);
+ Py_DECREF(tmp);
+ }
+ #endif
+ if (likely(v)) {
+ int one = 1; int is_little = (int)*(unsigned char *)&one;
+ unsigned char *bytes = (unsigned char *)&val;
+ int ret = _PyLong_AsByteArray((PyLongObject *)v,
+ bytes, sizeof(val),
+ is_little, !is_unsigned);
+ Py_DECREF(v);
+ if (likely(!ret))
+ return val;
+ }
+#endif
+ return (long) -1;
+ }
+ } else {
+ long val;
+ PyObject *tmp = __Pyx_PyNumber_Int(x);
+ if (!tmp) return (long) -1;
+ val = __Pyx_PyInt_As_long(tmp);
+ Py_DECREF(tmp);
+ return val;
+ }
+raise_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "value too large to convert to long");
+ return (long) -1;
+raise_neg_overflow:
+ PyErr_SetString(PyExc_OverflowError,
+ "can't convert negative value to long");
+ return (long) -1;
+}
+
+static int
+__pyx_typeinfo_cmp(__Pyx_TypeInfo *a, __Pyx_TypeInfo *b)
+{
+ int i;
+ if (!a || !b)
+ return 0;
+ if (a == b)
+ return 1;
+ if (a->size != b->size || a->typegroup != b->typegroup ||
+ a->is_unsigned != b->is_unsigned || a->ndim != b->ndim) {
+ if (a->typegroup == 'H' || b->typegroup == 'H') {
+ return a->size == b->size;
+ } else {
+ return 0;
+ }
+ }
+ if (a->ndim) {
+ for (i = 0; i < a->ndim; i++)
+ if (a->arraysize[i] != b->arraysize[i])
+ return 0;
+ }
+ if (a->typegroup == 'S') {
+ if (a->flags != b->flags)
+ return 0;
+ if (a->fields || b->fields) {
+ if (!(a->fields && b->fields))
+ return 0;
+ for (i = 0; a->fields[i].type && b->fields[i].type; i++) {
+ __Pyx_StructField *field_a = a->fields + i;
+ __Pyx_StructField *field_b = b->fields + i;
+ if (field_a->offset != field_b->offset ||
+ !__pyx_typeinfo_cmp(field_a->type, field_b->type))
+ return 0;
+ }
+ return !a->fields[i].type && !b->fields[i].type;
+ }
+ }
+ return 1;
+}
+
+static int
+__pyx_check_strides(Py_buffer *buf, int dim, int ndim, int spec)
+{
+ if (buf->shape[dim] <= 1)
+ return 1;
+ if (buf->strides) {
+ if (spec & __Pyx_MEMVIEW_CONTIG) {
+ if (spec & (__Pyx_MEMVIEW_PTR|__Pyx_MEMVIEW_FULL)) {
+ if (buf->strides[dim] != sizeof(void *)) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer is not indirectly contiguous "
+ "in dimension %d.", dim);
+ goto fail;
+ }
+ } else if (buf->strides[dim] != buf->itemsize) {
+ PyErr_SetString(PyExc_ValueError,
+ "Buffer and memoryview are not contiguous "
+ "in the same dimension.");
+ goto fail;
+ }
+ }
+ if (spec & __Pyx_MEMVIEW_FOLLOW) {
+ Py_ssize_t stride = buf->strides[dim];
+ if (stride < 0)
+ stride = -stride;
+ if (stride < buf->itemsize) {
+ PyErr_SetString(PyExc_ValueError,
+ "Buffer and memoryview are not contiguous "
+ "in the same dimension.");
+ goto fail;
+ }
+ }
+ } else {
+ if (spec & __Pyx_MEMVIEW_CONTIG && dim != ndim - 1) {
+ PyErr_Format(PyExc_ValueError,
+ "C-contiguous buffer is not contiguous in "
+ "dimension %d", dim);
+ goto fail;
+ } else if (spec & (__Pyx_MEMVIEW_PTR)) {
+ PyErr_Format(PyExc_ValueError,
+ "C-contiguous buffer is not indirect in "
+ "dimension %d", dim);
+ goto fail;
+ } else if (buf->suboffsets) {
+ PyErr_SetString(PyExc_ValueError,
+ "Buffer exposes suboffsets but no strides");
+ goto fail;
+ }
+ }
+ return 1;
+fail:
+ return 0;
+}
+static int
+__pyx_check_suboffsets(Py_buffer *buf, int dim, CYTHON_UNUSED int ndim, int spec)
+{
+ if (spec & __Pyx_MEMVIEW_DIRECT) {
+ if (buf->suboffsets && buf->suboffsets[dim] >= 0) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer not compatible with direct access "
+ "in dimension %d.", dim);
+ goto fail;
+ }
+ }
+ if (spec & __Pyx_MEMVIEW_PTR) {
+ if (!buf->suboffsets || (buf->suboffsets && buf->suboffsets[dim] < 0)) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer is not indirectly accessible "
+ "in dimension %d.", dim);
+ goto fail;
+ }
+ }
+ return 1;
+fail:
+ return 0;
+}
+static int
+__pyx_verify_contig(Py_buffer *buf, int ndim, int c_or_f_flag)
+{
+ int i;
+ if (c_or_f_flag & __Pyx_IS_F_CONTIG) {
+ Py_ssize_t stride = 1;
+ for (i = 0; i < ndim; i++) {
+ if (stride * buf->itemsize != buf->strides[i] &&
+ buf->shape[i] > 1)
+ {
+ PyErr_SetString(PyExc_ValueError,
+ "Buffer not fortran contiguous.");
+ goto fail;
+ }
+ stride = stride * buf->shape[i];
+ }
+ } else if (c_or_f_flag & __Pyx_IS_C_CONTIG) {
+ Py_ssize_t stride = 1;
+ for (i = ndim - 1; i >- 1; i--) {
+ if (stride * buf->itemsize != buf->strides[i] &&
+ buf->shape[i] > 1) {
+ PyErr_SetString(PyExc_ValueError,
+ "Buffer not C contiguous.");
+ goto fail;
+ }
+ stride = stride * buf->shape[i];
+ }
+ }
+ return 1;
+fail:
+ return 0;
+}
+static int __Pyx_ValidateAndInit_memviewslice(
+ int *axes_specs,
+ int c_or_f_flag,
+ int buf_flags,
+ int ndim,
+ __Pyx_TypeInfo *dtype,
+ __Pyx_BufFmt_StackElem stack[],
+ __Pyx_memviewslice *memviewslice,
+ PyObject *original_obj)
+{
+ struct __pyx_memoryview_obj *memview, *new_memview;
+ __Pyx_RefNannyDeclarations
+ Py_buffer *buf;
+ int i, spec = 0, retval = -1;
+ __Pyx_BufFmt_Context ctx;
+ int from_memoryview = __pyx_memoryview_check(original_obj);
+ __Pyx_RefNannySetupContext("ValidateAndInit_memviewslice", 0);
+ if (from_memoryview && __pyx_typeinfo_cmp(dtype, ((struct __pyx_memoryview_obj *)
+ original_obj)->typeinfo)) {
+ memview = (struct __pyx_memoryview_obj *) original_obj;
+ new_memview = NULL;
+ } else {
+ memview = (struct __pyx_memoryview_obj *) __pyx_memoryview_new(
+ original_obj, buf_flags, 0, dtype);
+ new_memview = memview;
+ if (unlikely(!memview))
+ goto fail;
+ }
+ buf = &memview->view;
+ if (buf->ndim != ndim) {
+ PyErr_Format(PyExc_ValueError,
+ "Buffer has wrong number of dimensions (expected %d, got %d)",
+ ndim, buf->ndim);
+ goto fail;
+ }
+ if (new_memview) {
+ __Pyx_BufFmt_Init(&ctx, stack, dtype);
+ if (!__Pyx_BufFmt_CheckString(&ctx, buf->format)) goto fail;
+ }
+ if ((unsigned) buf->itemsize != dtype->size) {
+ PyErr_Format(PyExc_ValueError,
+ "Item size of buffer (%" CYTHON_FORMAT_SSIZE_T "u byte%s) "
+ "does not match size of '%s' (%" CYTHON_FORMAT_SSIZE_T "u byte%s)",
+ buf->itemsize,
+ (buf->itemsize > 1) ? "s" : "",
+ dtype->name,
+ dtype->size,
+ (dtype->size > 1) ? "s" : "");
+ goto fail;
+ }
+ for (i = 0; i < ndim; i++) {
+ spec = axes_specs[i];
+ if (!__pyx_check_strides(buf, i, ndim, spec))
+ goto fail;
+ if (!__pyx_check_suboffsets(buf, i, ndim, spec))
+ goto fail;
+ }
+ if (buf->strides && !__pyx_verify_contig(buf, ndim, c_or_f_flag))
+ goto fail;
+ if (unlikely(__Pyx_init_memviewslice(memview, ndim, memviewslice,
+ new_memview != NULL) == -1)) {
+ goto fail;
+ }
+ retval = 0;
+ goto no_fail;
+fail:
+ Py_XDECREF(new_memview);
+ retval = -1;
+no_fail:
+ __Pyx_RefNannyFinishContext();
+ return retval;
+}
+
+static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_ds_nn_npy_double(PyObject *obj) {
+ __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } };
+ __Pyx_BufFmt_StackElem stack[1];
+ int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) };
+ int retcode;
+ if (obj == Py_None) {
+ result.memview = (struct __pyx_memoryview_obj *) Py_None;
+ return result;
+ }
+ retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0,
+ PyBUF_RECORDS, 1,
+ &__Pyx_TypeInfo_nn_npy_double, stack,
+ &result, obj);
+ if (unlikely(retcode == -1))
+ goto __pyx_fail;
+ return result;
+__pyx_fail:
+ result.memview = NULL;
+ result.data = NULL;
+ return result;
+}
+
+static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsdsds_nn_npy_uint8(PyObject *obj) {
+ __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } };
+ __Pyx_BufFmt_StackElem stack[1];
+ int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) };
+ int retcode;
+ if (obj == Py_None) {
+ result.memview = (struct __pyx_memoryview_obj *) Py_None;
+ return result;
+ }
+ retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0,
+ PyBUF_RECORDS, 3,
+ &__Pyx_TypeInfo_nn_npy_uint8, stack,
+ &result, obj);
+ if (unlikely(retcode == -1))
+ goto __pyx_fail;
+ return result;
+__pyx_fail:
+ result.memview = NULL;
+ result.data = NULL;
+ return result;
+}
+
+static CYTHON_INLINE __Pyx_memviewslice __Pyx_PyObject_to_MemoryviewSlice_dsds_nn_npy_uint8(PyObject *obj) {
+ __Pyx_memviewslice result = { 0, 0, { 0 }, { 0 }, { 0 } };
+ __Pyx_BufFmt_StackElem stack[1];
+ int axes_specs[] = { (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED), (__Pyx_MEMVIEW_DIRECT | __Pyx_MEMVIEW_STRIDED) };
+ int retcode;
+ if (obj == Py_None) {
+ result.memview = (struct __pyx_memoryview_obj *) Py_None;
+ return result;
+ }
+ retcode = __Pyx_ValidateAndInit_memviewslice(axes_specs, 0,
+ PyBUF_RECORDS, 2,
+ &__Pyx_TypeInfo_nn_npy_uint8, stack,
+ &result, obj);
+ if (unlikely(retcode == -1))
+ goto __pyx_fail;
+ return result;
+__pyx_fail:
+ result.memview = NULL;
+ result.data = NULL;
+ return result;
+}
+
+static int __Pyx_check_binary_version(void) {
+ char ctversion[4], rtversion[4];
+ PyOS_snprintf(ctversion, 4, "%d.%d", PY_MAJOR_VERSION, PY_MINOR_VERSION);
+ PyOS_snprintf(rtversion, 4, "%s", Py_GetVersion());
+ if (ctversion[0] != rtversion[0] || ctversion[2] != rtversion[2]) {
+ char message[200];
+ PyOS_snprintf(message, sizeof(message),
+ "compiletime version %s of module '%.100s' "
+ "does not match runtime version %s",
+ ctversion, __Pyx_MODULE_NAME, rtversion);
+ return PyErr_WarnEx(NULL, message, 1);
+ }
+ return 0;
+}
+
+#ifndef __PYX_HAVE_RT_ImportModule
+#define __PYX_HAVE_RT_ImportModule
+static PyObject *__Pyx_ImportModule(const char *name) {
+ PyObject *py_name = 0;
+ PyObject *py_module = 0;
+ py_name = __Pyx_PyIdentifier_FromString(name);
+ if (!py_name)
+ goto bad;
+ py_module = PyImport_Import(py_name);
+ Py_DECREF(py_name);
+ return py_module;
+bad:
+ Py_XDECREF(py_name);
+ return 0;
+}
+#endif
+
+#ifndef __PYX_HAVE_RT_ImportType
+#define __PYX_HAVE_RT_ImportType
+static PyTypeObject *__Pyx_ImportType(const char *module_name, const char *class_name,
+ size_t size, int strict)
+{
+ PyObject *py_module = 0;
+ PyObject *result = 0;
+ PyObject *py_name = 0;
+ char warning[200];
+ Py_ssize_t basicsize;
+#ifdef Py_LIMITED_API
+ PyObject *py_basicsize;
+#endif
+ py_module = __Pyx_ImportModule(module_name);
+ if (!py_module)
+ goto bad;
+ py_name = __Pyx_PyIdentifier_FromString(class_name);
+ if (!py_name)
+ goto bad;
+ result = PyObject_GetAttr(py_module, py_name);
+ Py_DECREF(py_name);
+ py_name = 0;
+ Py_DECREF(py_module);
+ py_module = 0;
+ if (!result)
+ goto bad;
+ if (!PyType_Check(result)) {
+ PyErr_Format(PyExc_TypeError,
+ "%.200s.%.200s is not a type object",
+ module_name, class_name);
+ goto bad;
+ }
+#ifndef Py_LIMITED_API
+ basicsize = ((PyTypeObject *)result)->tp_basicsize;
+#else
+ py_basicsize = PyObject_GetAttrString(result, "__basicsize__");
+ if (!py_basicsize)
+ goto bad;
+ basicsize = PyLong_AsSsize_t(py_basicsize);
+ Py_DECREF(py_basicsize);
+ py_basicsize = 0;
+ if (basicsize == (Py_ssize_t)-1 && PyErr_Occurred())
+ goto bad;
+#endif
+ if (!strict && (size_t)basicsize > size) {
+ PyOS_snprintf(warning, sizeof(warning),
+ "%s.%s size changed, may indicate binary incompatibility",
+ module_name, class_name);
+ if (PyErr_WarnEx(NULL, warning, 0) < 0) goto bad;
+ }
+ else if ((size_t)basicsize != size) {
+ PyErr_Format(PyExc_ValueError,
+ "%.200s.%.200s has the wrong size, try recompiling",
+ module_name, class_name);
+ goto bad;
+ }
+ return (PyTypeObject *)result;
+bad:
+ Py_XDECREF(py_module);
+ Py_XDECREF(result);
+ return NULL;
+}
+#endif
+
+static int __Pyx_InitStrings(__Pyx_StringTabEntry *t) {
+ while (t->p) {
+ #if PY_MAJOR_VERSION < 3
+ if (t->is_unicode) {
+ *t->p = PyUnicode_DecodeUTF8(t->s, t->n - 1, NULL);
+ } else if (t->intern) {
+ *t->p = PyString_InternFromString(t->s);
+ } else {
+ *t->p = PyString_FromStringAndSize(t->s, t->n - 1);
+ }
+ #else
+ if (t->is_unicode | t->is_str) {
+ if (t->intern) {
+ *t->p = PyUnicode_InternFromString(t->s);
+ } else if (t->encoding) {
+ *t->p = PyUnicode_Decode(t->s, t->n - 1, t->encoding, NULL);
+ } else {
+ *t->p = PyUnicode_FromStringAndSize(t->s, t->n - 1);
+ }
+ } else {
+ *t->p = PyBytes_FromStringAndSize(t->s, t->n - 1);
+ }
+ #endif
+ if (!*t->p)
+ return -1;
+ ++t;
+ }
+ return 0;
+}
+
+static CYTHON_INLINE PyObject* __Pyx_PyUnicode_FromString(const char* c_str) {
+ return __Pyx_PyUnicode_FromStringAndSize(c_str, (Py_ssize_t)strlen(c_str));
+}
+static CYTHON_INLINE char* __Pyx_PyObject_AsString(PyObject* o) {
+ Py_ssize_t ignore;
+ return __Pyx_PyObject_AsStringAndSize(o, &ignore);
+}
+static CYTHON_INLINE char* __Pyx_PyObject_AsStringAndSize(PyObject* o, Py_ssize_t *length) {
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII || __PYX_DEFAULT_STRING_ENCODING_IS_DEFAULT
+ if (
+#if PY_MAJOR_VERSION < 3 && __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ __Pyx_sys_getdefaultencoding_not_ascii &&
+#endif
+ PyUnicode_Check(o)) {
+#if PY_VERSION_HEX < 0x03030000
+ char* defenc_c;
+ PyObject* defenc = _PyUnicode_AsDefaultEncodedString(o, NULL);
+ if (!defenc) return NULL;
+ defenc_c = PyBytes_AS_STRING(defenc);
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ {
+ char* end = defenc_c + PyBytes_GET_SIZE(defenc);
+ char* c;
+ for (c = defenc_c; c < end; c++) {
+ if ((unsigned char) (*c) >= 128) {
+ PyUnicode_AsASCIIString(o);
+ return NULL;
+ }
+ }
+ }
+#endif
+ *length = PyBytes_GET_SIZE(defenc);
+ return defenc_c;
+#else
+ if (__Pyx_PyUnicode_READY(o) == -1) return NULL;
+#if __PYX_DEFAULT_STRING_ENCODING_IS_ASCII
+ if (PyUnicode_IS_ASCII(o)) {
+ *length = PyUnicode_GET_LENGTH(o);
+ return PyUnicode_AsUTF8(o);
+ } else {
+ PyUnicode_AsASCIIString(o);
+ return NULL;
+ }
+#else
+ return PyUnicode_AsUTF8AndSize(o, length);
+#endif
+#endif
+ } else
+#endif
+#if !CYTHON_COMPILING_IN_PYPY
+ if (PyByteArray_Check(o)) {
+ *length = PyByteArray_GET_SIZE(o);
+ return PyByteArray_AS_STRING(o);
+ } else
+#endif
+ {
+ char* result;
+ int r = PyBytes_AsStringAndSize(o, &result, length);
+ if (unlikely(r < 0)) {
+ return NULL;
+ } else {
+ return result;
+ }
+ }
+}
+static CYTHON_INLINE int __Pyx_PyObject_IsTrue(PyObject* x) {
+ int is_true = x == Py_True;
+ if (is_true | (x == Py_False) | (x == Py_None)) return is_true;
+ else return PyObject_IsTrue(x);
+}
+static CYTHON_INLINE PyObject* __Pyx_PyNumber_Int(PyObject* x) {
+ PyNumberMethods *m;
+ const char *name = NULL;
+ PyObject *res = NULL;
+#if PY_MAJOR_VERSION < 3
+ if (PyInt_Check(x) || PyLong_Check(x))
+#else
+ if (PyLong_Check(x))
+#endif
+ return Py_INCREF(x), x;
+ m = Py_TYPE(x)->tp_as_number;
+#if PY_MAJOR_VERSION < 3
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Int(x);
+ }
+ else if (m && m->nb_long) {
+ name = "long";
+ res = PyNumber_Long(x);
+ }
+#else
+ if (m && m->nb_int) {
+ name = "int";
+ res = PyNumber_Long(x);
+ }
+#endif
+ if (res) {
+#if PY_MAJOR_VERSION < 3
+ if (!PyInt_Check(res) && !PyLong_Check(res)) {
+#else
+ if (!PyLong_Check(res)) {
+#endif
+ PyErr_Format(PyExc_TypeError,
+ "__%.4s__ returned non-%.4s (type %.200s)",
+ name, name, Py_TYPE(res)->tp_name);
+ Py_DECREF(res);
+ return NULL;
+ }
+ }
+ else if (!PyErr_Occurred()) {
+ PyErr_SetString(PyExc_TypeError,
+ "an integer is required");
+ }
+ return res;
+}
+static CYTHON_INLINE Py_ssize_t __Pyx_PyIndex_AsSsize_t(PyObject* b) {
+ Py_ssize_t ival;
+ PyObject *x;
+#if PY_MAJOR_VERSION < 3
+ if (likely(PyInt_CheckExact(b)))
+ return PyInt_AS_LONG(b);
+#endif
+ if (likely(PyLong_CheckExact(b))) {
+ #if CYTHON_COMPILING_IN_CPYTHON && PY_MAJOR_VERSION >= 3
+ #if CYTHON_USE_PYLONG_INTERNALS
+ switch (Py_SIZE(b)) {
+ case -1: return -(sdigit)((PyLongObject*)b)->ob_digit[0];
+ case 0: return 0;
+ case 1: return ((PyLongObject*)b)->ob_digit[0];
+ }
+ #endif
+ #endif
+ return PyLong_AsSsize_t(b);
+ }
+ x = PyNumber_Index(b);
+ if (!x) return -1;
+ ival = PyInt_AsSsize_t(x);
+ Py_DECREF(x);
+ return ival;
+}
+static CYTHON_INLINE PyObject * __Pyx_PyInt_FromSize_t(size_t ival) {
+ return PyInt_FromSize_t(ival);
+}
+
+
+#endif /* Py_PYTHON_H */
diff --git a/partfinder/_tiger.pxd b/partfinder/_tiger.pxd
new file mode 100644
index 0000000..3646992
--- /dev/null
+++ b/partfinder/_tiger.pxd
@@ -0,0 +1,40 @@
+"""
+Definitions for c++ or boost classes
+"""
+from libcpp.vector cimport vector
+from libcpp.string cimport string
+# from libcpp.utility cimport pair
+# from libcpp.cast import dynamic_cast, static_cast
+# from libcpp.set cimport set as std_set
+# from libcpp.map cimport map as std_map
+
+cdef extern from "<boost/dynamic_bitset.hpp>" namespace "boost":
+ cdef cppclass dynamic_bitset[T]:
+ dynamic_bitset(size_t)
+ void resize(size_t)
+ void set(size_t)
+ void reset(size_t)
+ void flip(size_t)
+
+ size_t size()
+ bint test(size_t)
+ bint empty()
+ bint all()
+ bint any()
+ bint none()
+ size_t count()
+ bint is_subset_of(dynamic_bitset[T]&)
+ bint is_proper_subset_of(dynamic_bitset[T]&)
+ bint intersects(dynamic_bitset[T]& a)
+
+ cdef void to_string(dynamic_bitset[size_t], string s)
+
+ctypedef dynamic_bitset[size_t] c_Bitset
+ctypedef vector[c_Bitset] c_ColumnBitsets
+ctypedef vector[c_ColumnBitsets] c_AlignmentBitsets
+
+cdef class TigerBase:
+ cdef:
+ c_AlignmentBitsets _bitsets
+ readonly:
+ size_t species_count, column_count
diff --git a/partfinder/_tiger.pyx b/partfinder/_tiger.pyx
new file mode 100644
index 0000000..eecd337
--- /dev/null
+++ b/partfinder/_tiger.pyx
@@ -0,0 +1,125 @@
+# distutils: include_dirs = NUMPY_PATH
+# cython: wraparound=False
+# cython: cdivision=True
+# cython: boundscheck=False
+#
+# from _utility cimport dynamic_bitset
+cimport numpy as np
+
+import cython
+import numpy
+import copy
+import sys
+import numpy
+from cython.operator import dereference as deref, preincrement as preinc
+
+cdef class TigerBase:
+ def __cinit__(self):
+ pass
+
+ def calc_rates(self):
+ if self.species_count == 0 or self.column_count == 0:
+ return None
+
+ rates = numpy.zeros(self.column_count, dtype='f8')
+ cdef:
+ size_t i, j, i_b, j_b
+ double rate, axpi, num, denom
+ c_Bitset *i_bitset
+ c_Bitset *j_bitset
+ np.npy_double[:] c_rates = rates
+
+ denom = <double>self.column_count - 1.0
+ for i in range(self.column_count):
+ rate = 0.0
+ for j in range(self.column_count):
+ # Don't compare to self
+ if i == j:
+ continue
+
+ num = 0.0
+ axpi = 0.0
+ for j_b in range(4):
+ j_bitset = &self._bitsets[j][j_b]
+ if j_bitset.none():
+ continue
+ num += 1.0
+ for i_b in range(4):
+ i_bitset = &self._bitsets[i][i_b]
+ if i_bitset.none():
+ continue
+ if j_bitset.is_subset_of(deref(i_bitset)):
+ axpi += 1.0
+ break
+
+ rate += axpi / num
+
+ rate /= denom
+ c_rates[i] = rate
+
+ return rates
+
+ def bitsets_as_array(self):
+ if self.species_count == 0 or self.column_count == 0:
+ return None
+
+ ret = numpy.zeros((self.column_count, 4, self.species_count), dtype='u1')
+ cdef:
+ np.npy_uint8[:, :, :] c_ret = ret
+ size_t i, j, k
+
+ for i in range(self.column_count):
+ for j in range(4):
+ for k in range(self.species_count):
+ if self._bitsets[i][j].test(k):
+ c_ret[i, j, k] = 1
+ return ret
+
+cdef class TigerDNA(TigerBase):
+ def __cinit__(self):
+ self.species_count = 0
+ self.column_count = 0
+
+ def build_bitsets(self, alignment):
+ cdef:
+ size_t i, j, k, sp_count, col_count
+ np.npy_uint8[:, :] data = alignment.data
+ unsigned char c
+ c_Bitset *A_bits
+ c_Bitset *C_bits
+ c_Bitset *G_bits
+ c_Bitset *T_bits
+
+ sp_count, col_count = alignment.data.shape
+ self.species_count = sp_count
+ self.column_count = col_count
+
+ # Create all the bitsets
+ # NOTE: would be better if we could rely on emplace_back...
+ for i in range(col_count):
+ self._bitsets.push_back(c_ColumnBitsets())
+ for k in range(4):
+ self._bitsets.back().push_back(c_Bitset(sp_count))
+
+ for i in range(col_count):
+ A_bits = &self._bitsets[i][0]
+ C_bits = &self._bitsets[i][1]
+ G_bits = &self._bitsets[i][2]
+ T_bits = &self._bitsets[i][3]
+ for j in range(sp_count):
+ c = data[j, i]
+ if c == 'A':
+ A_bits.set(j)
+ elif c == 'C':
+ C_bits.set(j)
+ elif c == 'G':
+ G_bits.set(j)
+ elif c == 'T':
+ T_bits.set(j)
+ elif c == 'N' or c == '?' or c == '-':
+ A_bits.set(j)
+ C_bits.set(j)
+ G_bits.set(j)
+ T_bits.set(j)
+
+
diff --git a/partfinder/algorithm.py b/partfinder/algorithm.py
new file mode 100644
index 0000000..510e3c2
--- /dev/null
+++ b/partfinder/algorithm.py
@@ -0,0 +1,106 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+from math import sqrt
+from itertools import izip
+
+
+def k_subsets_i(n, k):
+ '''
+ http://code.activestate.com/recipes/500268-all-k-subsets-from-an-n-set/
+ Yield each subset of size k from the set of intergers 0 .. n - 1
+ n -- an integer > 0
+ k -- an integer > 0
+ '''
+ # Validate args
+ if n < 0:
+ raise ValueError('n must be > 0, got n=%d' % n)
+ if k < 0:
+ raise ValueError('k must be > 0, got k=%d' % k)
+ # check base cases
+ if k == 0 or n < k:
+ yield set()
+ elif n == k:
+ yield set(range(n))
+
+ else:
+ # Use recursive formula based on binomial coeffecients:
+ # choose(n, k) = choose(n - 1, k - 1) + choose(n - 1, k)
+ for s in k_subsets_i(n - 1, k - 1):
+ s.add(n - 1)
+ yield s
+ for s in k_subsets_i(n - 1, k):
+ yield s
+
+
+def k_subsets(s, k):
+ '''
+ http://code.activestate.com/recipes/500268-all-k-subsets-from-an-n-set/
+ Yield all subsets of size k from set (or list) s
+ s -- a set or list (any iterable will suffice)
+ k -- an integer > 0
+ '''
+ s = list(s)
+ n = len(s)
+ for k_set in k_subsets_i(n, k):
+ yield set([s[i] for i in k_set])
+
+
+def lumpings(scheme):
+ """
+ generate all possible lumpings of a given scheme, where a lumping involves
+ joining two partitions together scheme has to be a list of digits
+ """
+ # Get the numbers involved in the scheme
+ nums = set(scheme)
+ lumpings = []
+ for sub in k_subsets(nums, 2):
+ lump = list(scheme)
+ sub = list(sub)
+ sub.sort()
+ # Now replace all the instance of one number in lump with the other in
+ # sub
+ while lump.count(sub[1]) > 0:
+ lump[lump.index(sub[1])] = sub[0]
+ lumpings.append(lump)
+
+ return lumpings
+
+
+def euclidean_distance(x, y):
+ sum = 0
+ for xval, yval in izip(x, y):
+ sum += (xval - yval) ** 2
+ dist = sqrt(sum)
+ return dist
+
+
+def levels_to_scheme(levels, namedict):
+ """
+ take the return from Cluster.getlevel
+ and return it as a list of partition names description
+ """
+
+ levels = str(levels)
+
+ for key in namedict.keys():
+ old = str(namedict[key])
+ new = '"%s"' % key
+ levels = levels.replace(old, new)
+
+ levels = eval(levels)
+ return levels
diff --git a/partfinder/alignment.py b/partfinder/alignment.py
new file mode 100644
index 0000000..e711627
--- /dev/null
+++ b/partfinder/alignment.py
@@ -0,0 +1,442 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+"""Loading, Saving, Parsing Alignment Files
+
+ See the phyml details here:
+ http://www.atgc-montpellier.fr/phyml/usersguide.php?type=command
+
+"""
+import logtools
+log = logtools.get_logger()
+
+import os
+from util import PartitionFinderError
+import numpy
+import cStringIO
+
+# From the Phyml Website
+# http://www.atgc-montpellier.fr/phyml/usersguide.php?type=command
+valid_nucleotide = "AGCTUMRWSYKBDHVNX.-?"
+valid_amino = "ARNBDCQZEGHILKMFPSTWYVX.-?"
+
+
+class AlignmentError(PartitionFinderError):
+ pass
+
+
+class AlignmentParser(object):
+ def __init__(self, stream, valid_bases=None):
+ self.stream = stream
+ self.current_line = 0
+ self.cur_len = 0
+ self.start_base = 0
+ self.end_base = 0
+ self.valid_bases = valid_bases
+ self.block_len = None
+
+ # This is the stuff we'll copy across
+ self.species = []
+ self.species_count = 0
+ self.sequence_length = 0
+ self.data = None
+
+ def bases_to_array(self, bases=""):
+ upper_bases = bases.upper()
+ if self.valid_bases is not None:
+ should_be_empty = upper_bases.translate(None, self.valid_bases)
+ if should_be_empty != "":
+ log.error("Line %d: Invalid bases '%s' found.",
+ self.current_line, should_be_empty)
+ raise AlignmentError
+
+ # Which is faster?
+ # return array.array("B", upper_bases)
+ return numpy.fromstring(upper_bases, dtype='u1')
+
+ def parse(self):
+ # Parse the header...
+ self.parse_header()
+
+ # We now know how big it is, so allocate the array.
+ self.data = numpy.zeros((
+ self.species_count,
+ self.sequence_length
+ ), 'u1')
+
+ # Get the block with species in it
+ self.parse_species_block()
+
+ # Look for any further blocks
+ while self.parse_interleave_block():
+ pass
+
+ def parse_header(self):
+ while 1:
+ line = self.stream.readline()
+ self.current_line += 1
+
+ if len(line) == 0:
+ log.error("Line %d, Found no data in file", self.current_line)
+
+ # Skip blank lines
+ if len(line.strip()) == 0:
+ continue
+
+ # `split` works on whitespace
+ bits = line.split()
+
+ # We're looking for 2 bits, species count and bases
+ if len(bits) == 2:
+ # Convert them to integers
+ S, C = map(int, bits)
+ self.species_count = S
+ self.sequence_length = C
+ # We're done!
+ return
+ else:
+ log.error("""Line %d: Failed to find the Phyml header that
+ specifies the species count, and sequence length""",
+ self.current_line)
+ raise AlignmentError
+
+ def check_block(self):
+ # Do some checking on the line in the block
+ if self.block_len is None:
+ # Mark the length we got.
+ self.block_len = self.cur_len
+ self.end_base = self.start_base + self.block_len
+ if self.end_base > self.sequence_length + 1:
+ log.error("""Line %d: More supplied than defined in the
+ header""", self.current_line)
+ raise AlignmentError
+ else:
+ # Make sure all species report the same length.
+ if self.cur_len != self.block_len:
+ log.error("""Line %d: Number of bases differs in length
+ from previous line(s)""", self.current_line)
+ raise AlignmentError
+
+ def parse_species_block(self):
+ """Most sequences just have a block like this.
+
+ Species1 ATCT
+ Species2 ATCG
+ ...
+ """
+ self.block_len = None
+
+ # Look for species followed by bases, separated by whitespace.
+ cur_species = 0
+ while cur_species < self.species_count:
+ line = self.stream.readline()
+ self.current_line += 1
+
+ if len(line) == 0:
+ log.error("Line %d, Found no data in file", self.current_line)
+
+ bits = line.split()
+ num_bits = len(bits)
+ if num_bits == 0:
+ # Skip blanks lines
+ continue
+
+ # Should be two pieces -- [species, bases]
+ if len(bits) != 2:
+ log.error("""Line %d: Line should be species and bases
+ separated by whitespace""", self.current_line)
+ raise AlignmentError
+
+ spec, bases = bits
+ self.cur_len = len(bases)
+
+ self.check_block()
+ self.species.append(spec)
+
+ # Write into the array at the right position.
+ arr = self.bases_to_array(bases)
+ self.data[cur_species, self.start_base:self.end_base] = arr
+
+ cur_species += 1
+
+ self.start_base += self.block_len
+
+ def parse_interleave_block(self):
+ species_num = 0
+ blank_lines = 0
+ self.block_len = None
+
+ while species_num < self.species_count:
+ curline = self.stream.readline()
+ self.current_line += 1
+ self.cur_len = len(curline)
+
+ if self.cur_len == 0:
+ # If we read nothing, it is the end of the file
+ if species_num != 0:
+ log.error("""Line %d: "Did not find enough lines for all
+ species in interleave block""",
+ self.current_line)
+ raise AlignmentError
+ return False
+
+ # Strip any whitespace
+ bases = curline.strip()
+ self.cur_len = len(bases)
+
+ if self.cur_len == 0:
+ # Skip blanks
+ if species_num != 0:
+ log.error("""Line %d: Found blank line in interleave
+ block""", self.current_line)
+ raise AlignmentError
+
+ blank_lines += 1
+ continue
+
+ if blank_lines == 0:
+ log.error("""Line %d: Expected a blank line between blocks""",
+ self.current_line)
+ raise AlignmentError
+
+ self.check_block()
+
+ arr = self.bases_to_array(bases)
+ self.data[species_num, self.start_base:self.end_base] = arr
+
+ species_num += 1
+
+ self.start_base += self.block_len
+ return True
+
+
+class Alignment(object):
+ def __init__(self):
+ self.species = []
+ self.sequence_length = 0
+ self.data = None
+
+ @property
+ def species_count(self):
+ return len(self.species)
+
+ def __str__(self):
+ return "Alignment(%s species, %s bases)"\
+ % (self.species_count, self.sequence_length)
+
+ def same_as(self, other):
+ if self.sequence_length != other.sequence_length:
+ log.warning("Alignments not the same, length differs %s: %s",
+ self.sequence_length, other.sequence_length)
+ return False
+
+ if self.species_count != other.species_count:
+ log.warning("""Alignments not the same. This alignment has %s
+ species, the alignment from the previous analysis had
+ %s.""",
+ len(self.species), len(other.species))
+ return False
+
+ if not (self.data == other.data).all():
+ log.warning("Alignments not the same. Some of sequence differs.")
+ return False
+
+ return True
+
+ def parse_stream(self, stream):
+ p = AlignmentParser(stream)
+ p.parse()
+
+ # Copy everything from the import parser
+ self.sequence_length = p.sequence_length
+ self.species = p.species
+ self.data = p.data
+
+ def read(self, pth):
+ log.info("Reading alignment file '%s'", pth)
+ if not os.path.exists(pth):
+ log.error("Cannot find alignment file '%s'", pth)
+ raise AlignmentError
+
+ with open(pth, 'rU') as stream:
+ self.parse_stream(stream)
+
+ def parse(self, text):
+ stream = cStringIO.StringIO(text)
+ self.parse_stream(stream)
+
+ def write(self, pth):
+ fd = open(pth, 'w')
+ log.debug("Writing phylip file '%s'", pth)
+ self.write_phylip(fd)
+ fd.close()
+
+ def write_phylip(self, stream):
+ species_count = len(self.species)
+ stream.write("%d %d\n" % (species_count, self.sequence_length))
+ for i in range(species_count):
+ spec = self.species[i]
+ sequence = self.data[i]
+ # We use a version of phylip which can have longer species names,
+ # up to 100
+ shortened = "%s " % (spec[:99])
+ stream.write(shortened)
+ stream.write(sequence.tostring())
+ stream.write("\n")
+
+
+class SubsetAlignment(Alignment):
+ """Create an alignment based on some others and a subset definition"""
+
+ def __init__(self, source, subset):
+ """create an alignment for this subset"""
+ Alignment.__init__(self)
+
+ # Let's do a basic check to make sure that the specified sites
+ # aren't > alignment length
+ site_max = max(subset.columns) + 1
+ log.debug("Max site in data_blocks: %d; max site in alignment: %d"
+ % (site_max, source.sequence_length))
+ if site_max > source.sequence_length:
+ log.error("Site %d is specified in [data_blocks], "
+ "but the alignment only has %d sites. "
+ "Please check." % (site_max, source.sequence_length))
+ raise AlignmentError
+
+ self.species = source.species
+ # Pull out the columns we need using the magic of numpy indexing
+ self.data = source.data[:, subset.columns]
+ self.sequence_length = len(subset.columns)
+ assert self.sequence_length == self.data.shape[1]
+
+
+class TestAlignment(Alignment):
+ """Good for testing stuff"""
+ def __init__(self, text):
+ Alignment.__init__(self)
+ self.parse(text)
+
+
+def check_state_probs(Alignment, subset, cfg):
+
+ # there's no problem if the user doesn't care
+ # about how many states are in a subset
+ if cfg.all_states == False:
+ return False
+
+ sub_aln = SubsetAlignment(Alignment, subset)
+
+
+ dna_states = set('ACGT')
+ amino_states = set(['Alanine',
+ 'Arginine',
+ 'Asparagine',
+ 'Aspartic acid',
+ 'Cysteine',
+ 'Glutamine',
+ 'Glutamic acid',
+ 'Glycine',
+ 'Histidine',
+ 'Isoleucine',
+ 'Leucine',
+ 'Lysine',
+ 'Methionine',
+ 'Phenylalanine',
+ 'Proline',
+ 'Serine',
+ 'Threonine',
+ 'Tryptophan',
+ 'Tyrosine',
+ 'Valine'])
+
+
+ dna_dict = {'A': set('A'),
+ 'G': set('G'),
+ 'C': set('C'),
+ 'T': set('T'),
+ 'U': set('T'),
+ 'M': set('AC'),
+ 'R': set('AG'),
+ 'W': set('AT'),
+ 'S': set('CG'),
+ 'Y': set('CT'),
+ 'K': set('GT'),
+ 'B': set('CGT'),
+ 'D': set('AGT'),
+ 'H': set('ACT'),
+ 'V': set('ACG'),
+ 'N': set(''),
+ '?': set(''),
+ '-': set('')
+ }
+
+ amino_dict = {'A': set(['Alanine']),
+ 'R': set(['Arginine']),
+ 'N': set(['Asparagine']),
+ 'B': set(['Asparagine']),
+ 'D': set(['Aspartic acid']),
+ 'C': set(['Cysteine']),
+ 'Q': set(['Glutamine']),
+ 'Z': set(['Glutamine']),
+ 'E': set(['Glutamic acid']),
+ 'G': set(['Glycine']),
+ 'H': set(['Histidine']),
+ 'I': set(['Isoleucine']),
+ 'L': set(['Leucine']),
+ 'K': set(['Lysine']),
+ 'M': set(['Methionine']),
+ 'F': set(['Phenylalanine']),
+ 'P': set(['Proline']),
+ 'S': set(['Serine']),
+ 'T': set(['Threonine']),
+ 'W': set(['Tryptophan']),
+ 'Y': set(['Tyrosine']),
+ 'V': set(['Valine']),
+ 'X': set([]),
+ '?': set([]),
+ '-': set([])
+ }
+
+ # 1. Get set of all states in the alignment, obs([])
+ observed_states = numpy.unique(sub_aln.data).tostring()
+
+ # 2. run through all states
+ # for each state, extend a set of observed states, e.g. obs.add(x)
+ expanded_states = set([])
+ if cfg.datatype == 'protein':
+ all_states = amino_states
+ state_dict = amino_dict
+ elif cfg.datatype == 'DNA':
+ all_states = dna_states
+ state_dict = dna_dict
+
+ for state in observed_states:
+ try:
+ ex = state_dict[state]
+ except: #just in case
+ ex = set(state)
+
+ expanded_states = expanded_states.union(ex)
+
+ #3. Compare set of observed states to set of all states.
+ # If all states are in the observed states, return TRUE
+ # else return FALSE.
+ if len(all_states.difference(expanded_states)) > 0:
+ # some states are missing
+ return True
+ else:
+ return False
\ No newline at end of file
diff --git a/partfinder/analysis.py b/partfinder/analysis.py
new file mode 100644
index 0000000..ecfc65d
--- /dev/null
+++ b/partfinder/analysis.py
@@ -0,0 +1,295 @@
+# Copyright (C) 2012-2013 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import shutil
+from database import Database
+
+from alignment import Alignment, SubsetAlignment
+import threadpool
+import scheme
+import subset_ops
+import results
+import threading
+import collections
+from config import the_config
+from util import PartitionFinderError, ExternalProgramError
+import util
+
+class AnalysisError(PartitionFinderError):
+ pass
+
+
+class Analysis(object):
+ """Performs the analysis and collects the results"""
+ def __init__(self, cfg, force_restart, threads):
+ the_config.validate()
+
+ # TODO: Remove -- put this all into "options"
+ if threads == -1:
+ threads = threadpool.get_cpu_count()
+
+ self.threads = threads
+
+ # TODO: Move these to the config validate and prepare
+ log.info("Beginning Analysis")
+ self.process_restart(force_restart)
+
+ # Make some folders for the analysis
+ the_config.make_output_folders()
+ the_config.database = Database(the_config)
+
+ # Check for old analyses to see if we can use the old data
+ the_config.check_for_old_config()
+
+ # TODO: This is going to be in "Prepare"
+ self.make_alignment(cfg.alignment_path)
+ self.make_tree(cfg.user_tree_topology_path)
+
+ # We need this to block the threads for critical stuff
+ self.lock = threading.Condition(threading.Lock())
+
+ # Store the result in here
+ self.results = results.AnalysisResults(the_config.model_selection)
+
+ def process_restart(self, force_restart):
+ if force_restart:
+ # Remove everything
+ if os.path.exists(the_config.output_path):
+ log.warning("Deleting all previous workings in '%s'" %
+ the_config.output_path)
+ shutil.rmtree(the_config.output_path)
+ else:
+ # Remove the schemes folder, and clean out the phylofiles folder
+ if os.path.exists(the_config.schemes_path):
+ log.debug("Removing files in '%s'" % the_config.schemes_path)
+ shutil.rmtree(the_config.schemes_path)
+ if os.path.exists(the_config.phylofiles_path):
+ log.debug("Removing files in '%s'" % the_config.phylofiles_path)
+ shutil.rmtree(the_config.phylofiles_path)
+
+
+ def analyse(self):
+ try:
+ self.do_analysis()
+ finally:
+ # TODO: Not really the right place for it?
+ the_config.database.close()
+ return self.results
+
+
+
+ def make_alignment(self, source_alignment_path):
+ # Make the alignment
+ self.alignment = Alignment()
+ self.alignment.read(source_alignment_path)
+
+ # TODO REMOVE -- this should be part of the checking procedure
+ # We start by copying the alignment
+ self.alignment_path = os.path.join(the_config.start_tree_path, 'source.phy')
+ if os.path.exists(self.alignment_path):
+ # Make sure it is the same
+ old_align = Alignment()
+ old_align.read(self.alignment_path)
+ if not old_align.same_as(self.alignment):
+ log.error("""Alignment file has changed since previous run. You
+ need to use the force-restart option.""")
+ raise AnalysisError
+
+ compare = lambda x, y: collections.Counter(x) == collections.Counter(y)
+
+ if not compare(old_align.species, self.alignment.species):
+ log.error("""Species names in alignment have changed since previous run. You
+ need to use the force-restart option.""")
+ raise AnalysisError
+
+
+ else:
+ self.alignment.write(self.alignment_path)
+
+ def need_new_tree(self, tree_path):
+ if os.path.exists(tree_path):
+ if ';' in open(tree_path).read():
+ log.info("Starting tree file found.")
+ redo_tree = False
+ else:
+ log.info("""Starting tree file found but it is incomplete.
+ Re-estimating""")
+ redo_tree = True
+ else:
+ log.info("Starting tree will be estimated from the data.")
+ redo_tree = True
+
+ return redo_tree
+
+ def make_tree(self, user_path):
+ # Begin by making a filtered alignment, containing ONLY those columns
+ # that are defined in the subsets
+ subset_with_everything = subset_ops.merge_subsets(the_config.user_subsets)
+ self.filtered_alignment = SubsetAlignment(
+ self.alignment, subset_with_everything)
+ self.filtered_alignment_path = os.path.join(
+ the_config.start_tree_path, 'filtered_source.phy')
+ self.filtered_alignment.write(self.filtered_alignment_path)
+
+ # Check the full subset against the alignment
+ subset_ops.check_against_alignment(subset_with_everything, self.alignment)
+
+ # We start by copying the alignment
+ self.alignment_path = os.path.join(
+ the_config.start_tree_path, 'source.phy')
+
+ # Now check for the tree
+ tree_path = the_config.processor.make_tree_path(
+ self.filtered_alignment_path)
+
+ if self.need_new_tree(tree_path):
+ log.debug("Estimating new starting tree, no old tree found")
+
+ # If we have a user tree, then use that, otherwise, create a topology
+ util.clean_out_folder(the_config.start_tree_path,
+ keep=["filtered_source.phy", "source.phy"])
+
+ if user_path is not None and user_path != "":
+ # Copy it into the start tree folder
+ log.info("Using user supplied topology at %s" % user_path)
+ topology_path = os.path.join(the_config.start_tree_path, 'user_topology.phy')
+ util.dupfile(user_path, topology_path)
+ else:
+ log.debug(
+ "didn't find tree at %s, making a new one" % tree_path)
+ topology_path = the_config.processor.make_topology(
+ self.filtered_alignment_path, the_config.datatype, the_config.cmdline_extras)
+
+ # Now estimate branch lengths
+ tree_path = the_config.processor.make_branch_lengths(
+ self.filtered_alignment_path,
+ topology_path,
+ the_config.datatype,
+ the_config.cmdline_extras)
+
+ self.tree_path = tree_path
+ log.debug("Starting tree with branch lengths is here: %s" %
+ self.tree_path)
+
+ def run_task(self, model_name, sub):
+ # This bit should run in parallel (forking the processor)
+ try:
+ the_config.processor.analyse(
+ model_name,
+ sub.alignment_path,
+ self.tree_path,
+ the_config.branchlengths,
+ the_config.cmdline_extras
+ )
+ fabricate = False
+ except ExternalProgramError:
+ if not the_config.suppress_errors:
+ # In the Kmeans algorithm we suppress errors and "fabricate"
+ # subsets (we assume the error is because the subset is too
+ # small for analysis)
+ raise
+
+ # If it is kmeans we assume that the error is because the subset
+ # is too small or unanalysable, so we fabricate it
+ log.debug("New subset could not be analysed. It will be merged "
+ "at the end of the analysis")
+ fabricate = True
+
+ # Not entirely sure that WE NEED to block here, but it is safer to do
+ # It shouldn't hold things up toooo long...
+ self.lock.acquire()
+ try:
+ if fabricate:
+ sub.fabricate_model_result(the_config, model_name)
+ else:
+ sub.parse_model_result(the_config, model_name)
+
+ # Try finalising, then the result will get written out earlier...
+ sub.finalise(the_config)
+ finally:
+ self.lock.release()
+
+ def add_tasks_for_sub(self, tasks, sub):
+ for m in sub.models_to_process:
+ tasks.append((self.run_task, (m, sub)))
+
+ def run_concurrent(self, tasks):
+ for func, args in tasks:
+ func(*args)
+
+ def run_threaded(self, tasks):
+ if not tasks:
+ return
+ pool = threadpool.Pool(tasks, self.threads)
+ pool.join()
+
+ def analyse_list_of_subsets(self, subsets):
+ # get a whole list of subsets analysed in parallel
+
+ # analyse bigger subsets first, for efficiency
+ subsets.sort(key = lambda x: 1.0/float(len(x.columns)))
+
+ # prepare the list of tasks
+ tasks = []
+ for sub in subsets:
+ if sub.is_done:
+ pass
+ elif sub.is_prepared:
+ self.add_tasks_for_sub(tasks, sub)
+ else:
+ sub.prepare(the_config, self.alignment)
+ self.add_tasks_for_sub(tasks, sub)
+
+ if tasks:
+ # Now do the analysis
+ if self.threads == 1:
+ self.run_concurrent(tasks)
+ else:
+ self.run_threaded(tasks)
+
+ # Now see if we're done
+ for sub in subsets:
+ # ALL subsets should already be finalised in the task. We just
+ # check again here
+ if not sub.finalise(the_config):
+ log.error("Failed to run models %s; not sure why" %
+ ", " "".join(list(sub.models_not_done)))
+ raise AnalysisError
+
+ def analyse_scheme(self, sch):
+ # Progress
+ the_config.progress.next_scheme()
+
+ # analyse the subsets in the scheme that aren't done
+ # NB for most schemes we will have all subsets done, so this saves time
+ not_done = []
+ for sub in sch:
+ if sub.is_done == False:
+ not_done.append(sub)
+ if not_done:
+ self.analyse_list_of_subsets(not_done)
+
+ # AIC needs the number of sequences
+ number_of_seq = len(self.alignment.species)
+ result = scheme.SchemeResult(sch, number_of_seq, the_config.branchlengths, the_config.model_selection)
+ self.results.add_scheme_result(sch, result)
+
+ return result
diff --git a/partfinder/analysis_method.py b/partfinder/analysis_method.py
new file mode 100644
index 0000000..7aa7e86
--- /dev/null
+++ b/partfinder/analysis_method.py
@@ -0,0 +1,830 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import math
+import scheme
+import submodels
+from analysis import Analysis, AnalysisError
+import neighbour
+import kmeans
+import itertools
+import subset_ops
+from scipy import spatial, exp
+from scipy.misc import comb
+import numpy as np
+from config import the_config
+from alignment import SubsetAlignment, check_state_probs
+
+class UserAnalysis(Analysis):
+ def do_analysis(self):
+ log.info("Performing User analysis")
+ current_schemes = the_config.user_schemes
+ scheme_count = len(current_schemes)
+ subset_count = len(the_config.user_subsets)
+
+ the_config.progress.begin(scheme_count, subset_count)
+ if scheme_count > 0:
+ for s in current_schemes:
+ res = self.analyse_scheme(s)
+
+ # Write out the scheme
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(s, res)
+ else:
+ log.error(
+ "Search set to 'user', but no user schemes detected in .cfg file. Please check.")
+ raise AnalysisError
+
+ the_config.progress.end()
+
+ the_config.reporter.write_best_scheme(self.results)
+
+
+class StrictClusteringAnalysis(Analysis):
+ """
+ This analysis uses model parameters to guess at similar partitions, then
+ just joins them together this is much less accurate than other methods, but
+ a LOT quicker - it runs in order N time (where N is the number of initial
+ datablocks), whereas the greedy algorithm is still N squared.
+ """
+
+ def do_analysis(self):
+ log.info("Performing strict clustering analysis")
+
+ partnum = len(the_config.user_subsets)
+ subset_count = 2 * partnum - 1
+ scheme_count = partnum
+ the_config.progress.begin(scheme_count, subset_count)
+
+ # Start with the most partitioned scheme
+ start_description = range(partnum)
+ start_scheme = scheme.create_scheme(
+ the_config, "start_scheme", start_description)
+
+ # Analyse our first scheme
+ log.info("Analysing starting scheme (scheme %s)" % start_scheme.name)
+ self.analyse_scheme(start_scheme)
+
+ # Current scheme number
+ cur_s = 2
+
+ # Now we try out all clusterings of the first scheme, to see if we can
+ # find a better one
+ while True:
+ log.info("***Strict clustering algorithm step %d of %d***" %
+ (cur_s - 1, partnum - 1))
+
+ # Calculate the subsets which are most similar
+ # e.g. combined rank ordering of euclidean distances
+ # Could combine average site-rates, q matrices, and frequencies
+ scheme_name = "step_%d" % (cur_s - 1)
+ clustered_scheme = neighbour.get_nearest_neighbour_scheme(
+ start_scheme, scheme_name, the_config)
+
+ # Now analyse that new scheme
+ cur_s += 1
+ self.analyse_scheme(clustered_scheme)
+
+ # Stop when we've analysed the scheme with all subsets combined...
+ if len(set(clustered_scheme.subsets)) == 1:
+ # ... then it's the scheme with everything together
+ break
+ else:
+ # We keep going
+ start_scheme = clustered_scheme
+
+ the_config.progress.end()
+ the_config.reporter.write_best_scheme(self.results)
+
+
+class AllAnalysis(Analysis):
+ def do_analysis(self):
+ log.info("Performing complete analysis")
+ partnum = len(the_config.user_subsets)
+
+ scheme_count = submodels.count_all_schemes(partnum)
+ subset_count = submodels.count_all_subsets(partnum)
+ the_config.progress.begin(scheme_count, subset_count)
+
+ # Iterate over submodels, which we can turn into schemes afterwards in the loop
+ model_iterator = submodels.submodel_iterator([], 1, partnum)
+
+ scheme_name = 1
+ for m in model_iterator:
+ s = scheme.model_to_scheme(m, scheme_name, the_config)
+ scheme_name = scheme_name + 1
+ res = self.analyse_scheme(s)
+
+ # Write out the scheme
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(s, res)
+
+ the_config.reporter.write_best_scheme(self.results)
+
+
+class GreedyAnalysis(Analysis):
+
+ @logtools.log_info(log, "Performing Greedy Analysis")
+ def do_analysis(self):
+ '''A greedy algorithm for heuristic partitioning searches'''
+
+ partnum = len(the_config.user_subsets)
+ scheme_count = submodels.count_greedy_schemes(partnum)
+ subset_count = submodels.count_greedy_subsets(partnum)
+
+ the_config.progress.begin(scheme_count, subset_count)
+
+ # Start with the most partitioned scheme, and record it.
+ with logtools.indented(log, "*** Analysing starting scheme ***"):
+ the_config.progress.begin(scheme_count, partnum)
+ start_scheme = scheme.create_scheme(
+ the_config, "start_scheme", range(partnum))
+ start_result = self.analyse_scheme(start_scheme)
+ start_score = start_result.score
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(
+ self.results.best_scheme, self.results.best_result)
+
+ subsets = [s for s in start_scheme.subsets]
+
+ step = 1
+ while True:
+ with logtools.indented(log, "***Greedy algorithm step %d***" % step):
+ name_prefix = "step_%d" % (step)
+
+ # get distances between subsets
+ max_schemes = comb(len(start_scheme.subsets), 2)
+
+ # this is a fake distance matrix, so that the greedy algorithm
+ # can use all the tricks of the relaxed clustering algorithm
+ dim = len(subsets)
+ d_matrix = np.zeros((((dim*dim)-dim))/2)
+ d_matrix[:] = np.inf
+
+ if step == 1:
+ # Now initialise a change in info score matrix to inf
+ c_matrix = np.empty(d_matrix.shape)
+ c_matrix[:] = np.inf
+ c_matrix = spatial.distance.squareform(c_matrix)
+
+ # 1. pick top N subset pairs from distance matrix
+ cutoff = max_schemes
+
+ closest_pairs = neighbour.get_N_closest_subsets(
+ subsets, the_config, cutoff, d_matrix)
+
+ # 2. analyse subsets in top N that have not yet been analysed
+ pairs_todo = neighbour.get_pairs_todo(closest_pairs, c_matrix, subsets)
+ if len(pairs_todo)>0:
+ log.info("Analysing %d new subset pairs" % len(pairs_todo))
+ new_subs = []
+ sub_tuples = []
+ for pair in pairs_todo:
+ new_sub = subset_ops.merge_subsets(pair)
+ new_subs.append(new_sub)
+ sub_tuples.append((new_sub, pair))
+
+ the_config.progress.begin(scheme_count, len(new_subs))
+ self.analyse_list_of_subsets(new_subs)
+
+ # 3. for all K new subsets, update improvement matrix and find best pair
+ log.info("Finding the best partitioning scheme")
+ diffs = []
+ scheme_name = "step_%d" %(step)
+ for t in sub_tuples:
+ pair_merged = t[0]
+ pair = t[1]
+ new_scheme = neighbour.make_clustered_scheme(
+ start_scheme, scheme_name, pair, pair_merged, the_config)
+ r = self.analyse_scheme(new_scheme)
+ diff = r.score - start_score
+ diffs.append(diff)
+
+ c_matrix = neighbour.update_c_matrix(c_matrix, sub_tuples, subsets, diffs)
+
+
+ # 4. Find the best pair of subsets, and build a scheme based on that
+ # note that this matrix includes diagonals, which will all be zero
+ # since this is equivalent to comparing a scheme to itself.
+ # so we need to be careful to only proceed if we have a negative change
+ # which indicates an improvement in the score
+ best_change = np.amin(c_matrix)
+
+ log.debug("Biggest improvement in info score: %s", str(best_change))
+
+ if best_change>=0:
+ log.info("Found no schemes that improve the score, stopping")
+ break
+
+ best_pair = neighbour.get_best_pair(c_matrix, best_change, subsets)
+
+ best_merged = subset_ops.merge_subsets(best_pair)
+ best_scheme = neighbour.make_clustered_scheme(
+ start_scheme, scheme_name, best_pair, best_merged, the_config)
+ best_result = self.analyse_scheme(best_scheme)
+
+ # the best change can get updated a fraction at this point
+ # because calaculting the info score on the whole alignment
+ # is a little different from doing it on the one subset
+ best_change = self.results.best_score - start_score
+
+
+ log.info("Best scheme combines subsets: '%s' and '%s'" %(best_pair[0].name, best_pair[1].name))
+
+
+ log.info("The best scheme improves the %s score by %.2f to %.1f",
+ the_config.model_selection,
+ np.abs(best_change),
+ self.results.best_score)
+ start_scheme = best_scheme
+ start_score = best_result.score
+
+ log.debug("Best pair: %s", str([s.name for s in best_pair]))
+ log.debug("Merged into: %s", str([best_merged.name]))
+
+ # 5. reset_c_matrix and the subset list
+ c_matrix = neighbour.reset_c_matrix(c_matrix, list(best_pair), [best_merged], subsets)
+
+ # we updated the subset list in a special way, which matches how we update the c matrix:
+ subsets = neighbour.reset_subsets(subsets, list(best_pair), [best_merged])
+
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(
+ best_scheme, best_result)
+
+
+ if len(set(start_scheme.subsets)) == 1:
+ break
+
+ step += 1
+
+ log.info("Greedy algorithm finished after %d steps" % step)
+ log.info("Best scoring scheme is scheme %s, with %s score of %.3f"
+ % (self.results.best_scheme.name, the_config.model_selection,
+ self.results.best_score))
+
+ the_config.reporter.write_best_scheme(self.results)
+
+class RelaxedClusteringAnalysis(Analysis):
+ '''
+ A relaxed clustering algorithm for heuristic partitioning searches
+
+ 1. Rank subsets by their similarity (defined by clustering-weights)
+ 2. Analyse min(cluster-percent or cluster-max) most similar schemes
+ 3. Take the scheme that improves the AIC/BIC score the most
+ 4. Quit if no improvements.
+ '''
+
+ @logtools.log_info(log, "Performing relaxed clustering analysis")
+ def do_analysis(self):
+
+ # initialisation steps
+ model_selection = the_config.model_selection
+ partnum = len(the_config.user_subsets)
+
+ scheme_count = submodels.count_relaxed_clustering_schemes(
+ partnum, the_config.cluster_percent, the_config.cluster_max)
+ subset_count = submodels.count_relaxed_clustering_subsets(
+ partnum, the_config.cluster_percent, the_config.cluster_max)
+
+ log.info("PartitionFinder will have to analyse %d subsets to"
+ " complete this analyses" % subset_count)
+ the_config.progress.begin(scheme_count, subset_count)
+
+ # Start with the most partitioned scheme, and record it.
+ with logtools.indented(log, "*** Analysing starting scheme ***"):
+ the_config.progress.begin(scheme_count, partnum)
+ start_scheme = scheme.create_scheme(
+ the_config, "start_scheme", range(partnum))
+ start_result = self.analyse_scheme(start_scheme)
+ start_score = start_result.score
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(
+ self.results.best_scheme, self.results.best_result)
+
+ subsets = [s for s in start_scheme.subsets]
+
+ step = 1
+ while True:
+ with logtools.indented(log, "*** Relaxed clustering algorithm step %d of up to %d ***"
+ % (step, partnum - 1)):
+
+ # get distances between subsets
+ max_schemes = comb(len(start_scheme.subsets), 2)
+ log.info("Measuring the similarity of %d subset pairs" % max_schemes)
+ d_matrix = neighbour.get_distance_matrix(subsets,
+ the_config.cluster_weights)
+
+ if step == 1:
+ # Now initialise a change in info score matrix to inf
+ c_matrix = np.empty(d_matrix.shape)
+ c_matrix[:] = np.inf
+ c_matrix = spatial.distance.squareform(c_matrix)
+
+ # 1. pick top N subset pairs from distance matrix
+ cutoff = int(math.ceil(max_schemes * (the_config.cluster_percent * 0.01)))
+ if cutoff <= 0: cutoff = 1
+ if the_config.cluster_max != None and cutoff>the_config.cluster_max:
+ cutoff = the_config.cluster_max
+ log.info("Choosing the %d most similar subset pairs" % cutoff)
+ closest_pairs = neighbour.get_N_closest_subsets(
+ subsets, the_config, cutoff, d_matrix)
+
+ # 2. analyse K subsets in top N that have not yet been analysed
+ pairs_todo = neighbour.get_pairs_todo(closest_pairs, c_matrix, subsets)
+ if len(pairs_todo)>0:
+ log.info("Analysing %d new subset pairs" % len(pairs_todo))
+ new_subs = []
+ sub_tuples = []
+ for pair in pairs_todo:
+ new_sub = subset_ops.merge_subsets(pair)
+ new_subs.append(new_sub)
+ sub_tuples.append((new_sub, pair))
+
+ the_config.progress.begin(scheme_count, len(new_subs))
+ self.analyse_list_of_subsets(new_subs)
+
+ # 3. for all K new subsets, update improvement matrix and find best pair
+ log.info("Finding the best partitioning scheme")
+ diffs = []
+ scheme_name = "step_%d" %(step)
+ for t in sub_tuples:
+ pair_merged = t[0]
+ pair = t[1]
+ new_scheme = neighbour.make_clustered_scheme(
+ start_scheme, scheme_name, pair, pair_merged, the_config)
+ r = self.analyse_scheme(new_scheme)
+ diff = r.score - start_score
+ diffs.append(diff)
+
+ c_matrix = neighbour.update_c_matrix(c_matrix, sub_tuples, subsets, diffs)
+
+ # 4. Find the best pair of subsets, and build a scheme based on that
+ # note that this matrix includes diagonals, which will all be zero
+ # since this is equivalent to comparing a scheme to itself.
+ # so we need to be careful to only proceed if we have a negative change
+ # which indicates an improvement in the score
+ best_change = np.amin(c_matrix)
+
+ log.debug("Biggest improvement in info score: %s", str(best_change))
+
+ if best_change>=0:
+ log.info("Found no schemes that improve the score, stopping")
+ break
+
+ best_pair = neighbour.get_best_pair(c_matrix, best_change, subsets)
+
+ best_merged = subset_ops.merge_subsets(best_pair)
+ best_scheme = neighbour.make_clustered_scheme(
+ start_scheme, scheme_name, best_pair, best_merged, the_config)
+ best_result = self.analyse_scheme(best_scheme)
+
+ # the best change can get updated a fraction at this point
+ # because calaculting the info score on the whole alignment
+ # is a little different from doing it on the one subset
+ best_change = self.results.best_score - start_score
+
+
+ log.info("Best scheme combines subsets: '%s' and '%s'" %(best_pair[0].name, best_pair[1].name))
+
+
+ log.info("The best scheme improves the %s score by %.2f to %.1f",
+ the_config.model_selection,
+ np.abs(best_change),
+ self.results.best_score)
+ start_scheme = best_scheme
+ start_score = best_result.score
+
+ log.debug("Best pair: %s", str([s.name for s in best_pair]))
+ log.debug("Merged into: %s", str([best_merged.name]))
+
+ # 5. reset_c_matrix and the subset list
+ c_matrix = neighbour.reset_c_matrix(c_matrix, list(best_pair), [best_merged], subsets)
+
+ # we update the subset list in a way that means its structure tracks the c-matrix
+ subsets = neighbour.reset_subsets(subsets, list(best_pair), [best_merged])
+
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(
+ best_scheme, best_result)
+
+
+ if len(set(start_scheme.subsets)) == 1:
+ break
+
+ step += 1
+
+ log.info("Relaxed clustering algorithm finished after %d steps" % step)
+ log.info("Best scoring scheme is scheme %s, with %s score of %.3f"
+ % (self.results.best_scheme.name, model_selection,
+ self.results.best_score))
+
+ the_config.reporter.write_best_scheme(self.results)
+
+
+
+class KmeansAnalysis(Analysis):
+
+
+ def split_subsets(self, start_subsets, tree_path):
+ split_subs = {}
+ for i, sub in enumerate(start_subsets):
+
+ # here we can test if the alignment has all states:
+ state_probs = check_state_probs(self.alignment, sub, the_config)
+
+ if (
+ len(sub.columns) == 1 or
+ len(sub.columns) < the_config.min_subset_size or
+ state_probs == True or
+ sub.dont_split == True
+ ):
+ split_subs[sub] = [sub]
+ log.info("Subset %d: %d sites not splittable" %(i+1, len(sub.columns)))
+ else:
+ split = kmeans.kmeans_split_subset(
+ the_config, self.alignment, sub, tree_path, n_jobs=self.threads)
+
+ if split == 1: # we couldn't analyse the big subset
+ sub.dont_split = True # never try to split this subset again
+ split_subs[sub] = [sub] # so we keep it whole
+ log.info("Subset %d: %d sites not splittable" %(i+1, len(sub.columns)))
+
+ elif len(split) == 1:
+ # in some cases (i.e. all site params are equal) kmeans
+ # cannot split subsets, so we get back the same as we put in
+ sub.dont_split = True # never try to split this subset again
+ split_subs[sub] = [sub] # so we keep it whole
+ log.info("Subset %d: %d sites not splittable" %(i+1, len(sub.columns)))
+
+ elif min([len(split[0].columns), len(split[1].columns)]) < the_config.min_subset_size:
+ # we don't split it if either of the two daughter subset was
+ # smaller than the minimum allowable size
+ sub.dont_split = True # never try to split this subset again
+ split_subs[sub] = [sub] # so we keep it whole
+ log.info("Subset %d: %d sites not splittable" %(i+1, len(sub.columns)))
+
+ elif (
+ check_state_probs(self.alignment, split[0], the_config) == True or
+ check_state_probs(self.alignment, split[1], the_config) == True
+ ):
+ # we don't split it if either of the daughter subsets has problems with
+ # the state frequencies
+ sub.dont_split = True # never try to split this subset again
+ split_subs[sub] = [sub] # so we keep it whole
+ log.info("Subset %d: %d sites not splittable" %(i+1, len(sub.columns)))
+
+ else: # we could analyse the big subset
+ split_subs[sub] = split # so we split it into >1
+ log.info("Subset %d: %d sites split into %d and %d"
+ %(i+1, len(sub.columns), len(split[0].columns), len(split[1].columns)))
+
+ return split_subs
+
+ def finalise_fabrication(self, start_subsets, step):
+
+ fabricated_subsets = []
+ for s in start_subsets:
+
+ # here we put a sensible lower limit on the size of subsets
+ if len(s.columns)<the_config.min_subset_size:
+ s.fabricated = True
+ log.debug("Subset %s with only %d sites found" %(s.subset_id, len(s.columns)))
+
+ # here we can test if the alignment has all states:
+ state_probs = check_state_probs(self.alignment, s, the_config)
+ if state_probs == True:
+ s.fabricated = True
+ log.debug("Subset %s does not have all states in the alignment", s.subset_id)
+
+ if s.fabricated:
+ fabricated_subsets.append(s)
+ log.debug("added %s to fabricated subset", s.name)
+
+ if fabricated_subsets:
+ with logtools.indented(log, "Finalising partitioning scheme"):
+ log.debug("There are %d/%d fabricated subsets"
+ % (len(fabricated_subsets), len(start_subsets)))
+
+ i = 1
+ while fabricated_subsets:
+
+ all_subs = start_subsets
+
+ # occasionally subsets with all value == 0.0 are given a
+ # centroid of None by scikit-learn. The true entropy here
+ # is 0.0 for all sites, so the true centroid is 0.0
+ for s in all_subs:
+ if s.centroid == None:
+ s.centroid = [0.0]
+ log.debug("Fixed a subset with a centroid of None")
+ log.debug("The subset has %d columns" % len(s.columns))
+
+ s = fabricated_subsets.pop(0)
+
+ log.debug("Working on fabricated subset %s with %d sites" %(s.subset_id, len(s.columns)))
+ log.info("Finalising subset %d", i)
+ i = i+1
+
+ all_subs.remove(s)
+
+ centroid = s.centroid
+
+ best_match = None
+
+ # get closest subset to s
+ for sub in all_subs:
+
+ centroid_array = [sub.centroid, centroid]
+
+ euclid_dist = spatial.distance.pdist(centroid_array)
+
+ if euclid_dist < best_match or best_match is None:
+ best_match = euclid_dist
+ closest_sub = sub
+
+ # join s with closest_sub to make joined_sub
+ merged_sub = subset_ops.merge_subsets([s, closest_sub])
+
+ # remove closest sub
+ all_subs.remove(closest_sub)
+
+ # and if closest_sub was fabricated too, we remove it here
+ if fabricated_subsets.count(closest_sub):
+ fabricated_subsets.remove(closest_sub)
+
+ # analyse joined sub
+ self.analyse_list_of_subsets([merged_sub])
+
+ # here we put a sensible lower limit on the size of subsets
+ if len(merged_sub.columns)<the_config.min_subset_size:
+ merged_sub.fabricated = True
+
+ # if joined has to be fabricated, add to fabricated list
+ if merged_sub.fabricated:
+ fabricated_subsets.append(merged_sub)
+
+ all_subs.append(merged_sub)
+ else:
+ all_subs = start_subsets
+
+ # now build a scheme from start_subs, and it should work
+ final_scheme = scheme.Scheme(the_config, "final_scheme", all_subs)
+
+ # return final scheme
+ return final_scheme
+
+ def build_new_subset_list(self, name_prefix, split_subs, start_subsets):
+ new_scheme_subs = []
+ for i, sub in enumerate(start_subsets):
+ if len(sub.columns) == 1:
+ new_scheme_subs.append(sub)
+ log.debug("Split %d: parent subset has only one site, %s unchanged" %
+ (i+1, the_config.model_selection.upper()))
+
+ elif sub.fabricated or sub.dont_split:
+ new_scheme_subs.append(sub)
+ log.debug("Split %d: parent subset couldn't be analysed, %s unchanged" %
+ (i+1, the_config.model_selection.upper()))
+
+ else: # compare split to un-split
+ log.debug("Splitting new subset")
+
+ # get list of split subsets from dictionary
+ split_subsets = split_subs[sub]
+
+ log.debug("# subs in this split: %d" % len(split_subsets))
+ log.debug("dont_split: %s" % split_subsets[0].dont_split)
+
+ # split subsets might be fabricated (i.e. unanalyseable)
+ fabrications = 0
+ for s in split_subsets:
+ fabrications = fabrications + s.fabricated
+
+ if fabrications == 0:
+
+ score_diff = subset_ops.subset_list_score_diff(split_subsets, [sub], the_config, self.alignment)
+
+ log.info("Subset %d: split changed %s by: %.1f" %
+ (i+1, the_config.model_selection.upper(),
+ score_diff))
+
+ lnL, sum_k, subs_len = subset_ops.subset_list_stats([sub], the_config, self.alignment)
+
+ per_site_improvement = score_diff / subs_len
+
+ log.debug("Per site improvement: %.1f" % (per_site_improvement))
+
+ if score_diff < 0:
+ # We ONLY split the subset if the score improved and the LRT is significant
+ new_scheme_subs = new_scheme_subs + split_subsets
+ else:
+ sub.dont_split = True
+ new_scheme_subs.append(sub)
+ elif fabrications == len(split_subsets):
+ # none of the split subsets worked, so don't analyse the parent again
+ sub.dont_split = True
+ new_scheme_subs.append(sub)
+ log.info("No splittable subsets")
+ else:
+ new_scheme_subs = new_scheme_subs + split_subsets
+
+ return new_scheme_subs
+
+ def report(self, step):
+ # Since the AIC will likely be better before we dealt with the
+ # fabricated subsets, we need to set the best scheme and best result
+ # to those from the last merged_scheme. TODO: add a variable to scheme
+ # to take care of this problem so that the best AND analysable scheme
+ # is the one that gets automatically flagged as the best scheme
+ log.info("** Kmeans algorithm finished after %d steps **" % (step))
+ log.info("Best scoring scheme has %d subsets and a %s score of %.3f"
+ % (
+ len(self.results.best_scheme.subsets), the_config.model_selection,
+ self.results.best_score))
+ the_config.reporter.write_best_scheme(self.results)
+
+ def setup(self):
+
+ partnum = len(the_config.user_subsets)
+ the_config.progress.begin(1, 1)
+
+ # Start with the most partitioned scheme
+ start_description = range(partnum)
+ start_scheme = scheme.create_scheme(
+ the_config, "start_scheme", start_description)
+
+ if len(start_scheme.subsets)>1:
+ log.error("The k-means algorithm is designed to analyse \
+ the entire alignment at once. To use it, please define a \
+ single data block that includes all of your sites, and \
+ again."
+ )
+ raise AnalysisError
+
+ site_max = sum([ len(s.columns) for s in start_scheme.subsets])
+
+ if the_config.min_subset_size > site_max:
+ log.error("The minimum subset size must be smaller than the \
+ total number of sites you want to analyse. Your minimum \
+ subset size is %d, and your alignment is %d sites. Please \
+ check and try again." %(the_config.min_subset_size, site_max)
+ )
+ raise AnalysisError
+
+
+ with logtools.indented(log, "**Analysing starting scheme (scheme %s)**" % start_scheme.name):
+ start_result = self.analyse_scheme(start_scheme)
+
+ if not the_config.quick:
+ the_config.reporter.write_scheme_summary(start_scheme, start_result)
+
+ tree_path = the_config.processor.make_tree_path(
+ self.filtered_alignment_path)
+
+ if the_config.kmeans == 'tiger':
+ try:
+ from _tiger import TigerDNA
+ the_config.TigerDNA = TigerDNA
+ except:
+ log.error("Couldn't find compiled tiger code.")
+ log.error("You have selected kmeans and tiger \
+ rates. This is an unsupported option, if you still wish to use \
+ this option, you must compile the tiger code.")
+ log.error("Once you compile the tiger code, this option will work. \
+ But please note that this is an \
+ unsupported option. For empirical work we recommend using \
+ entropy calculations for site rates, which is the default \
+ behaviour for the kmeans algorithm in PF2.")
+ raise AnalysisError
+ else:
+ the_config.TigerDNA = None
+
+
+ return start_result, start_scheme, tree_path
+
+ def one_kmeans_step(self, start_subsets, step, tree_path):
+ name_prefix = "step_%d" % (step)
+
+ # 1. Make split subsets
+
+ with logtools.indented(log, "Splitting subsets using k-means"):
+ split_subs = self.split_subsets(start_subsets, tree_path)
+
+ # 2. Analyse split subsets (this to take advantage of parallelisation)
+ subs = []
+
+ # make a list from the dictionary
+ for vals in split_subs.values():
+ subs.extend(vals)
+
+
+ log.debug("%d subsets successfully split" %(len(subs) - len(start_subsets)))
+
+ with logtools.indented(log, "Calculating scores of all new subsets that can be analysed"):
+ self.analyse_list_of_subsets(subs)
+
+ # 3. Build new list of subsets
+ new_scheme_subs = self.build_new_subset_list(name_prefix, split_subs, start_subsets)
+
+
+ # 4. Are we done yet?
+ if len(new_scheme_subs) == len(list(start_subsets)):
+ log.info("""Could not improve %s score. Algorithm finished."""
+ % (the_config.model_selection))
+ done = True
+ else:
+ n_splits = len(new_scheme_subs) - len(start_subsets)
+
+ if n_splits > 1:
+ t = 'subsets'
+ else:
+ t = 'subset'
+ log.info("""The %s score of %d %s
+ improved when split"""
+ % (the_config.model_selection, n_splits, t))
+
+ start_subsets = new_scheme_subs
+
+ done = False
+
+ return done, start_subsets
+
+ @logtools.log_info(log, "Performing k-means Analysis")
+ def do_analysis(self):
+ '''A kmeans algorithm for heuristic partitioning searches'''
+
+ start_result, start_scheme, tree_path = self.setup()
+
+ step = 0
+
+ start_subsets = list(start_scheme.subsets) # we only work on lists of subsets
+
+ self.analyse_list_of_subsets(start_subsets)
+
+ # now we suppress ExternalProgramError for the rest of the algorithm
+ the_config.suppress_errors = True
+
+ for s in start_subsets:
+ if s.fabricated:
+ log.error("""One or more of your starting datablocks could not
+ be analysed. Please check your data and try again.
+ One way to fix this is to join your small datablocks
+ together into larger datablocks""")
+ raise AnalysisError
+
+ while True:
+ step += 1
+ with logtools.indented(log, "***k-means algorithm step %d***"
+ % step):
+ done, start_subsets = self.one_kmeans_step(
+ start_subsets, step, tree_path)
+
+ if done:
+ break
+
+ # Ok, we're done. we just need deal with fabricated subsets
+ final_scheme = self.finalise_fabrication(start_subsets, step)
+
+ log.info("Analysing final scheme")
+ final_result = self.analyse_scheme(final_scheme)
+
+ self.report(step)
+
+ return(final_scheme)
+
+
+def choose_method(search):
+ if search == 'all':
+ method = AllAnalysis
+ elif search == 'user':
+ method = UserAnalysis
+ elif search == 'greedy':
+ method = GreedyAnalysis
+ elif search == 'hcluster':
+ method = StrictClusteringAnalysis
+ elif search == 'rcluster':
+ method = RelaxedClusteringAnalysis
+ elif search == 'kmeans':
+ method = KmeansAnalysis
+ else:
+ log.error("Search algorithm '%s' is not recognised", search)
+ raise AnalysisError
+ return method
diff --git a/partfinder/config.py b/partfinder/config.py
new file mode 100644
index 0000000..48f04ee
--- /dev/null
+++ b/partfinder/config.py
@@ -0,0 +1,478 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import logging
+import os
+import fnmatch
+import scheme
+import subset
+import parser
+import util
+import progress
+import cPickle as pickle
+
+class ConfigurationError(util.PartitionFinderError):
+ pass
+
+
+class Configuration(object):
+ # List of valid options. The first one is the default
+ options = {
+ 'branchlengths': ['linked', 'unlinked'],
+ 'model_selection': ['aic', 'aicc', 'bic'],
+ 'search': ['all', 'user', 'greedy', 'hcluster', 'rcluster', 'kmeans']
+ }
+
+ def __init__(self):
+ pass
+
+ def init(self, datatype="DNA", phylogeny_program='phyml',
+ save_phylofiles=False, cmdline_extras="", cluster_weights=None,
+ cluster_percent=10.0, cluster_max=1000, kmeans='entropy', quick=False, min_subset_size = 100, all_states = False):
+
+
+ log.info("------------- Configuring Parameters -------------")
+ # Only required if user adds them
+ self.user_schemes = scheme.SchemeSet()
+ self.user_subsets = []
+ self.user_subsets_by_name = {}
+ self.models = []
+ self.database = None
+ self.suppress_errors = False
+
+ self.save_phylofiles = save_phylofiles
+ self.progress = progress.NoProgress(self)
+ self.cmdline_extras = cmdline_extras
+ self.cluster_percent = float(cluster_percent)
+ self.cluster_max = cluster_max
+ self.kmeans = kmeans
+ self.quick = quick
+ self.min_subset_size = min_subset_size
+ self.all_states = all_states
+
+
+ # Record this
+ self.base_path = '.'
+ self.alignment = None
+ self.user_tree = None
+ self.old_working_directory = None
+ self.model_count = 0
+
+ # Some basic checking of the setup, so that we don't hit too many
+ # problems later
+
+
+
+
+ if datatype != "DNA" and datatype != "protein":
+ log.error("datatype must be 'DNA' or 'protein'")
+ raise ConfigurationError
+
+ log.info("Setting datatype to '%s'", datatype)
+ self.datatype = datatype
+
+ if phylogeny_program != "phyml" and phylogeny_program != "raxml":
+ log.error("Phylogeny program must be 'phyml' or 'raxml'")
+ raise ConfigurationError
+
+ # Import the right processor
+ self.processor = __import__(phylogeny_program.lower(), globals())
+
+ # This returns the record layout for the results that we store. It
+ # varies depending on the processor, and also DNA vs protein
+ self.data_layout = self.processor.make_data_layout(self)
+
+ log.info("Setting phylogeny program to '%s'", phylogeny_program)
+ self.phylogeny_program = phylogeny_program
+
+ # Now find the phylogeny_program before we do any changing of dirs
+ self.find_programs()
+
+ self.set_default_options()
+
+ # TODO: Move all these horrible functions somewhere else. This should be done
+ # elsewhere in the option setting
+ self.validate_cluster_weights(cluster_weights)
+ self.validate_cluster()
+ self.validate_kmeans()
+
+
+ return self
+
+
+
+ def set_default_options(self):
+
+ # Set the defaults into the class. These can be reset by calling
+ # set_option(...)
+ for o, v in self.options.items():
+ # Could call self.set_option here -- but it might confuse users
+ setattr(self, o, v[0])
+
+ def validate_cluster_weights(self, cluster_weights):
+ if cluster_weights is None:
+ # default weights - just use overall rates of subsets. Based on
+ # 2013 analyses.
+ self.cluster_weights = {"rate": 1, "freqs": 0,
+ "model": 0, "alpha": 0}
+ else:
+ # TODO. Is there a more robust way to do this...
+ # Brett say "YES. But this will do for now..."
+ cluster_weights = [x.strip() for x in cluster_weights.split(",")]
+
+ # now we check that it's a list of exactly four numbers
+ if len(cluster_weights) != 4:
+ log.error("Your --cluster_weights argument should have exactly 4"
+ " numbers separated by commas, but it has %d ('%s') "
+ "Please check and try again", len(cluster_weights), cluster_weights)
+ raise ConfigurationError
+
+ total = 0.0
+ for thing in cluster_weights:
+ try:
+ num = float(thing)
+ assert num >= 0.0
+ except:
+ log.error("Unable to understand your --cluster_weights argument."
+ " It should look like this: --cluster_weights '1,2,3,6'. "
+ "Please double check that you included quotes, "
+ "and four numbers greater than or equal to zero "
+ "separated by commas. Then try again. "
+ "The part that I couldn't understand is this: '%s'" % thing)
+ raise ConfigurationError
+ total = total + num
+
+ if total==0.0:
+ log.error("Please provide at least one cluster weight greater than zero")
+
+ log.info("Setting cluster_weights to: "
+ "subset_rate = %s, freqs = %s, model = %s, alpha %s"
+ % (cluster_weights[0], cluster_weights[1],
+ cluster_weights[2], cluster_weights[3]))
+
+ self.cluster_weights = {}
+ self.cluster_weights["rate"] = float(eval(cluster_weights[0]))
+ self.cluster_weights["freqs"] = float(eval(cluster_weights[1]))
+ self.cluster_weights["model"] = float(eval(cluster_weights[2]))
+ self.cluster_weights["alpha"] = float(eval(cluster_weights[3]))
+
+ def validate_cluster(self):
+ try:
+ assert self.cluster_percent >= 0.0
+ assert self.cluster_percent <= 100.0
+ except:
+ log.error("The rcluster-percent variable must be between 0.0 to 100.0, yours "
+ "is %.2f. Please check and try again." % self.cluster_percent)
+ raise ConfigurationError
+ log.debug("Setting rcluster-percent to %.2f" % self.cluster_percent)
+
+ if self.cluster_max == -1:
+ # allow users to ignore cluster_max by passing in a -1
+ self.cluster_max = None
+
+ if self.cluster_max != None:
+ self.cluster_max = int(self.cluster_max)
+ try:
+ assert self.cluster_max > 0
+ except:
+ log.error("The rcluster-max variable must greater than zero, yours "
+ "is %d. Please check and try again." % self.cluster_max)
+ raise ConfigurationError
+ log.debug("Setting rcluster-max to %d" % self.cluster_max)
+
+ def validate_kmeans(self):
+ if self.kmeans not in ('entropy', 'fast_tiger', 'tiger'):
+ log.error(
+ "The --kmeans setting must be 'entropy', 'fast_tiger' \
+ or 'tiger'. Please check and restart")
+ raise ConfigurationError
+
+ def find_programs(self):
+ pth = os.path.abspath(__file__)
+ # Split off the name and the directory...
+ pth, notused = os.path.split(pth)
+ pth, notused = os.path.split(pth)
+ pth = os.path.join(pth, "programs")
+ pth = os.path.normpath(pth)
+ self.program_path = pth
+
+ # TODO This is bullshit---Need to make the config global
+ util.program_path = pth
+ log.info("Program path is here %s", self.program_path)
+
+ def reset(self):
+ if self.old_working_directory is not None:
+ log.debug(
+ "Returning to original path: %s", self.old_working_directory)
+ os.chdir(self.old_working_directory)
+ log.debug(
+ "Cleaning out all subsets (There are %d)...", subset.count_subsets())
+ subset.clear_subsets()
+ if self.database:
+ self.database.close()
+
+ def find_config_file(self, pth):
+ """Try and get the base folder and config file from the path"""
+ if os.path.isfile(pth):
+ # Is it a config file
+ pth, ext = os.path.splitext(pth)
+ folder, filename = os.path.split(pth)
+ filename += ext
+ if ext == '.cfg':
+ return folder, filename
+ # We still need a filename
+ else:
+ folder = pth
+
+ util.check_folder_exists(folder)
+
+ # Now let's find the filename. Just return the first hit.
+ for filename in os.listdir(folder):
+ if fnmatch.fnmatch(filename, '*.cfg'):
+ return folder, filename
+
+ log.error("Cannot find a configuration file in "
+ "working folder '%s'", folder)
+
+ raise ConfigurationError
+
+ def load_base_path(self, pth):
+ """Load using a base path folder"""
+ # Allow for user and environment variables
+ pth = os.path.expanduser(pth)
+ pth = os.path.expandvars(pth)
+ pth = os.path.normpath(pth)
+
+ folder, filename = self.find_config_file(pth)
+
+ # check that user didn't enter a file instead of a folder
+ # if os.path.isfile(pth):
+ # log.error("The second argument of the commandline currently
+ # points to a file, but it should point to the folder that contains
+ # the alignment and .cfg files, please check.")
+ # raise ConfigurationError
+
+ self.set_base_path(folder)
+
+ # From now on we refer to relative paths
+ config_path = os.path.join(self.base_path, filename)
+ log.debug("About to search for partition_finder.cfg file...")
+ config_path = os.path.join(self.base_path, "partition_finder.cfg")
+ util.check_file_exists(config_path)
+
+ self._output_folders = []
+ self.register_output_folders()
+
+ self.init_logger(self.base_path)
+ self.load(config_path)
+
+ def register_folder(self, name):
+ # Separate the naming and construction of folders
+ new_path = os.path.join(self.output_path, name)
+ self._output_folders.append(new_path)
+ setattr(self, name + "_path", new_path)
+
+ def make_output_folders(self):
+ util.make_dir(self.output_path)
+ for pth in self._output_folders:
+ util.make_dir(pth)
+
+ def register_output_folders(self):
+ self.register_folder('subsets')
+ self.register_folder('schemes')
+ self.register_folder('phylofiles')
+ self.register_folder('start_tree')
+
+ def init_logger(self, pth):
+ handler = logging.FileHandler(os.path.join(pth, "log.txt"), 'a')
+ formatter = logging.Formatter(
+ "%(levelname)-8s | %(asctime)s | %(name)-10s | %(message)s")
+ handler.setFormatter(formatter)
+ handler.setLevel(logging.DEBUG)
+ logging.getLogger("").addHandler(handler)
+
+ def load(self, config_path):
+ """We get the parser to construct the configuration"""
+ log.info("Loading configuration at '%s'", config_path)
+ self.config_path = config_path
+ p = parser.Parser(self)
+ p.parse_file(config_path)
+
+ log.info(
+ "------------------------ BEGINNING NEW RUN -------------------------------")
+
+ def set_base_path(self, base_path):
+ self.full_base_path = os.path.abspath(base_path)
+ log.info("Setting working folder to: '%s'", self.full_base_path)
+
+ # Now make our working folder this folder. All of our other paths will
+ # be relative to this
+ self.old_working_directory = os.getcwd()
+ os.chdir(self.full_base_path)
+
+ # Our base path is now this
+ self.base_path = '.'
+ self.output_path = os.path.join(self.base_path, "analysis")
+ self.full_output_path = os.path.join(self.full_base_path, "analysis")
+
+ def set_alignment_file(self, align):
+ log.info("Setting 'alignment' to '%s'", align)
+ self.alignment = align
+
+ def set_option(self, option, value):
+ # Make everything lowercase, this makes life easier for us
+ value = value.lower()
+
+ if option not in self.options:
+ log.error("'%s' is not a valid option to set in the configuration",
+ option)
+ raise ConfigurationError
+
+ # Compare lower case
+ valid = [x.lower() for x in self.options[option]]
+ if value not in valid:
+ log.error("'%s' is not a valid option for '%s'" % (value, option))
+ log.info("The only valid options for '%s' are: %s" %
+ (option, "'%s'" % ("', '".join(self.options[option]))))
+ raise ConfigurationError
+
+ # TODO: not the best place for this at all..., but it works
+ if option == "search" and "cluster" in value and self.phylogeny_program != 'raxml':
+ log.error("Clustering methods are only available when using raxml"
+ " (the --raxml commandline option). Please check and try again."
+ " See the manual for more details.")
+ raise ConfigurationError
+
+ log.info("Setting '%s' to '%s'", option, value)
+ setattr(self, option, value)
+
+ def validate(self):
+ """Should be called before processing"""
+ # Just path validation for now.
+ util.check_folder_exists(self.base_path)
+ self.alignment_path = os.path.join(self.base_path, self.alignment)
+ log.info("Looking for alignment file '%s'...", self.alignment_path)
+ util.check_file_exists(self.alignment_path)
+ if self.user_tree is None:
+ self.user_tree_topology_path = None
+ else:
+ self.user_tree_topology_path = \
+ os.path.join(self.base_path, self.user_tree)
+ log.info("Looking for tree file '{}'...".format(
+ self.user_tree_topology_path))
+ util.check_file_exists(self.user_tree_topology_path)
+
+ def check_for_old_config(self):
+ """
+ Check whether the analysis dictated by cfg has been run before, and if
+ the config has changed in any way that would make re-running it
+ invalid
+ """
+ # The important stuff in our analysis, that can't change if we want to re-use old subsets
+ if self.user_tree is None:
+ topology = ""
+ else:
+ topology = open(self.user_tree_topology_path).read()
+
+ datablocks = [(s.names, s.description, s.column_set) for s in self.user_subsets]
+
+ restart_info = {
+ 'alignment' : self.alignment,
+ 'branchlengths': self.branchlengths,
+ 'program' : self.phylogeny_program,
+ 'datablocks' : datablocks,
+ 'topology' : topology,
+ # self.partitions.partitions,
+ }
+
+ # We need to know if there's anything in the Database
+ has_subsets = not self.database.is_empty()
+
+ # We also need to know if there's an old conifg file saved
+ cfg_dir = os.path.join(self.output_path, 'cfg')
+ old_cfg_path = os.path.join(cfg_dir, 'oldcfg.bin')
+ if os.path.exists(old_cfg_path):
+ has_config = True
+ else:
+ has_config = False
+
+ if not has_subsets:
+ # We have no subsets so can't screw anything up, just copy the new
+ # cfg file settings, overwrite anything else
+ if not os.path.exists(cfg_dir):
+ os.makedirs(cfg_dir)
+ #store a nice binary
+ f = open(old_cfg_path, 'wb')
+ pickle.dump(restart_info, f, -1)
+ f.close()
+ return 0
+
+ if not has_config:
+ log.error("There are subsets stored, but PartitionFinder can't determine where they are from")
+ log.info("Please re-run the analysis using the '--force-restart' option at the command line")
+ log.warning("This will delete all of the analyses in the '/analysis' folder")
+ raise ConfigurationError
+
+ # We have an old config, load it and compare the important bits
+ log.info("Checking previously run configuration data...")
+ f = open(old_cfg_path, 'rb')
+ old_restart_info = pickle.load(f)
+ f.close()
+ fail = []
+
+ # if len(old_restart_info) != len(restart_info):
+ # log.error("Your old configuration doesn't match with your new one")
+ # log.error("The most common cause of this error is trying to run a half-finished analysis"
+ # " but switching PartitionFinder versions half way through")
+ # log.error("The solution is to either go back to the same version of PartitionFinder"
+ # " you used for the initial analysis, or to re-run the analysis using the "
+ # "--force-restart option at the command line.")
+
+ if not old_restart_info['alignment'] == restart_info['alignment']:
+ log.error("The alignment has changed between runs")
+ fail.append("alignment")
+
+ if not old_restart_info['branchlengths'] == restart_info['branchlengths']:
+ fail.append("branchlengths")
+
+ if not old_restart_info['datablocks'] == restart_info['datablocks']:
+ fail.append("[data_blocks]")
+
+ if not old_restart_info['program'] == restart_info['program']:
+ fail.append(
+ "phylogeny_program (the --raxml commandline option)")
+ #
+ if not old_restart_info['topology'] == restart_info['topology']:
+ fail.append("user_tree_topology")
+
+ if len(fail) > 0:
+ log.error("There are subsets stored, but PartitionFinder has detected that these were run using a different .cfg setup")
+ log.error("The following settings in the new .cfg file are incompatible with the previous analysis: %s" % (', '.join(fail)))
+ log.info("To run this analysis and overwrite previous output, re-run the analysis using '--force-restart' option")
+ log.info("To run this analysis without deleting the previous analysis, please place your alignment and .cfg in a new folder and try again")
+ raise ConfigurationError
+
+
+
+the_config = Configuration()
+
+def init(*args, **kwargs):
+ the_config.init(*args, **kwargs)
+ return the_config
diff --git a/partfinder/database.py b/partfinder/database.py
new file mode 100644
index 0000000..7988301
--- /dev/null
+++ b/partfinder/database.py
@@ -0,0 +1,168 @@
+# Copyright (C) 2012-2013 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import numpy
+import tables
+from itertools import combinations
+
+import raxml_models
+import phyml_models
+
+int_type = numpy.int32
+float_type = numpy.float32
+
+
+def _model_string_maxlen():
+ """Calculate the field size needed for model ids"""
+ # hardcoded for convenience. Could be dynamically set in future.
+ # the current longest is: BLOSUM62+I+G+X, i.e. 14 chars.
+ # so we just over double it, for safety
+
+ return 30
+
+
+class DataLayout(object):
+ def __init__(self, letters=None):
+ self.letters = letters
+ if letters is not None:
+ self.make_results_and_freqs()
+ else:
+ # We just fake an entry,
+ self.letter_indexes = { 'EMPTY': 0 }
+ self.rate_indexes = { 'EMPTY': 0 }
+ self.letter_size = 1
+ self.rate_size = 1
+
+ self.data_type = self.make_datatype()
+
+ def make_results_and_freqs(self):
+ l = list(self.letters)
+ self.letter_indexes = dict(zip(l, range(len(l))))
+ self.letter_size = len(self.letter_indexes)
+
+ ri = {}
+ for i, rate in enumerate(combinations(l, 2)):
+ # We need both directions as either could be used to look it up
+ # ie. A <-> C or C <-> A
+ f, t = rate
+ ri["%s_%s" % (f, t)] = i
+ ri["%s_%s" % (t, f)] = i
+
+ self.rate_indexes = ri
+ self.rate_size = len(ri) / 2
+
+ def get_empty_record(self):
+ return numpy.zeros(1, self.data_type)
+
+ def make_datatype(self):
+ # 32 is the md5 length
+ subset_id_length = 32
+ model_id_length = _model_string_maxlen()
+
+ layout = [
+ ('subset_id', 'S{}'.format(subset_id_length)),
+ ('model_id', 'S{}'.format(model_id_length)),
+ ('seconds', int_type),
+ ('params', int_type),
+ ]
+
+ # Now add the floating point fields
+ flds = "lnl alpha aic aicc bic site_rate".split()
+ for f in flds:
+ layout.append((f, float_type))
+
+ # Now add frequencies and rate. These are added as embedded in an extra dimension
+
+ layout.extend([
+ ('freqs', float_type, self.letter_size),
+ ('rates', float_type, self.rate_size),
+ ])
+
+ # Now construct the numpy datatype that gives us the layout
+ return numpy.dtype(layout)
+
+
+class DataRecord(object):
+ def __init__(self, cfg):
+ self.__dict__['_data'] = cfg.data_layout.get_empty_record()
+
+ def __getattr__(self, name):
+ return self._data[name]
+
+ def __setattr__(self, name, value):
+ self._data[name] = value
+
+ def __str__(self):
+ return "DataRecord<lnl:%s, tree_size:%s, secs:%s>" % (
+ self.lnl, self.site_rate, self.seconds)
+
+
+class Database(object):
+
+ def __init__(self, cfg):
+ self.cfg = cfg
+ self.path = os.path.join(self.cfg.subsets_path, 'data.db')
+ self.results = None
+ if os.path.exists(self.path):
+ try:
+ self.h5 = tables.open_file(self.path, 'a')
+ self.results = self.h5.root.results
+ except:
+ # If anything fails, we just create a new database...
+ log.warning("""Failed to open existing database at %s, or
+ database is corrupted. Creating a new one""", self.path)
+ self.results = None
+
+ # Something went wrong!
+ if not self.results:
+ try:
+ # Try closing this, just in case
+ self.h5.close()
+ except:
+ pass
+
+ # Compression is good -- and faster, according to the pytables docs...
+ f = tables.Filters(complib='blosc', complevel=5)
+ self.h5 = tables.open_file(self.path, 'w', filters=f)
+ self.results = self.h5.create_table(
+ '/', 'results', cfg.data_layout.data_type)
+ self.results.cols.subset_id.create_csindex()
+
+ assert isinstance(self.results, tables.Table)
+ assert self.results.indexed
+
+ def get_results_for_subset(self, subset):
+ conditions = {'current_id': subset.subset_id}
+ matching = self.results.read_where(
+ 'subset_id == current_id', conditions)
+ return matching
+
+ def is_empty(self):
+ return self.results.nrows == 0
+
+ def save_result(self, subset, n):
+ # We have to take a slice here, as pytables can't handle single
+ # elements
+ self.results.append(subset.result_array[n:n+1])
+ self.cfg.database.results.flush()
+
+ def close(self):
+ self.h5.close()
diff --git a/partfinder/entropy.py b/partfinder/entropy.py
new file mode 100644
index 0000000..0ecaf97
--- /dev/null
+++ b/partfinder/entropy.py
@@ -0,0 +1,101 @@
+# Copyright (C) 2012-2013 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+from alignment import Alignment
+import numpy as np
+from config import the_config
+from util import PartitionFinderError
+
+# defining a new function 'entropy_calc' which takes as input a 1D array p
+# copied from here: http://nbviewer.ipython.org/url/atwallab.cshl.edu/teaching/QBbootcamp3.ipynb
+def entropy_calc(p):
+ p=p[p!=0] # modify p to include only those elements that are not equal to 0
+ return np.dot(-p,np.log2(p)) # the function returns the entropy result
+
+
+def get_morph_entropies(alignment):
+ morph_align = alignment.T
+ column_counts = []
+ for col in morph_align:
+ new_col = col[col != ord('-')]
+ new_col = new_col[new_col != ord('?')]
+ column_counts.append(np.unique(new_col, return_counts=True)[1])
+ column_entropy = []
+ for col in column_counts:
+ sum = np.sum(col)
+ props = np.array([num/float(sum) for num in col])
+ column_entropy.append(entropy_calc(props))
+ column_entropy = np.array(column_entropy)
+ return column_entropy
+
+def sitewise_entropies(alignment):
+ if the_config.datatype == 'DNA':
+ log.debug("Calculating DNA entropies")
+ dna_states = "ACGT"
+ dna_list = [np.sum(alignment.data == ord(nuc), axis = 0) for nuc in list(dna_states)]
+ states = np.array(dna_list, dtype=float)
+
+ elif the_config.datatype == 'protein':
+ log.debug("Calculating protein entropies")
+ aa_states = "ARNDCQEGHILKMFPSTWYV"
+ amino_list = [np.sum(alignment.data == ord(aa), axis = 0) for aa in list(aa_states)]
+ states = np.array(amino_list, dtype = float)
+ elif the_config.datatype == 'morphology':
+ return(get_morph_entropies(alignment))
+ else:
+ log.error("Unknown datatype '%s'" % the_config.datatype)
+ raise PartitionFinderError
+
+ states = states.T
+ totals = np.sum(states, axis=1)
+ totals.shape = len(states),1
+
+ # for a column of all gaps, we'll have a zero total, so we just hack that here
+ totals = np.where(totals==0, 1, totals)
+
+ prob = states/totals
+
+ column_entropy = [[entropy_calc(t)] for t in prob]
+
+ column_entropy = np.array(column_entropy)
+
+ return column_entropy
+
+def sitewise_entropies_scaled(alignment):
+ """This function will calculate entropies for DNA based on the assumption
+ that the states in the column are the only possible states, i.e. it
+ doesn't assume four states for each column
+ """
+ dna_align = alignment.data.T
+ column_counts = []
+ for col in dna_align:
+ new_col = col[col != ord('-')]
+ new_col = new_col[new_col != ord('?')]
+ column_counts.append(np.unique(new_col, return_counts=True)[1])
+ column_entropy = []
+ for col in column_counts:
+ sum = np.sum(col)
+ props = np.array([num/float(sum) for num in col])
+ column_entropy.append([entropy_calc(props)])
+ column_entropy = np.array(column_entropy)
+ return column_entropy
+
+
+
diff --git a/partfinder/kmeans.py b/partfinder/kmeans.py
new file mode 100644
index 0000000..6678918
--- /dev/null
+++ b/partfinder/kmeans.py
@@ -0,0 +1,175 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import time
+
+import numpy as np
+from sklearn.cluster import KMeans
+from sklearn.preprocessing import scale
+from collections import defaultdict
+from alignment import SubsetAlignment
+import util
+from config import the_config
+import entropy
+import sys
+from util import PartitionFinderError
+
+import subset_ops
+
+# You can run kmeans in parallel, specify n_jobs as -1 and it will run
+# on all cores available.
+def kmeans(rate_array, number_of_ks, n_jobs):
+ '''Take as input a list of sites, performs k-means clustering on
+ sites and returns k centroids and a dictionary with k's as keys
+ and lists of sites belonging to that k as values
+ '''
+ log.debug("Beginning k-means splitting")
+ start = time.clock()
+
+ # Create and scale an array for input into kmeans function
+ array = scale(rate_array)
+
+ # Call scikit_learn's k-means, use "k-means++" to find centroids
+ # kmeans_out = KMeans(init='k-means++', n_init = 100)
+ kmeans_out = KMeans(init='k-means++', n_clusters=number_of_ks,
+ n_init=100, n_jobs=n_jobs, random_state = 2147483647)
+ # Perform k-means clustering on the array of site likelihoods
+ kmeans_out.fit(array)
+
+ # Retrieve centroids
+ centroids = kmeans_out.cluster_centers_
+ # Add all centroids to a list to return
+ centroid_list = [list(centroid) for centroid in centroids]
+
+ # Retrieve a list with the cluster number for each site
+ rate_categories = kmeans_out.labels_
+ rate_categories = list(rate_categories)
+
+ # Transpose the list of cluster numbers to a dictionary with
+ # cluster numbers as keys and list of sites belonging to that
+ # cluster as the value
+ cluster_dict = defaultdict(list)
+ for num in range(len(rate_categories)):
+ cluster_dict[rate_categories[num]].append(num + 1)
+
+ stop = time.clock()
+ time_taken = "k-means splitting took %s seconds" % (stop - start)
+ log.debug(time_taken)
+
+ # Return centroids and dictionary with lists of sites for each k
+ return centroid_list, dict(cluster_dict)
+
+def rate_parser(rates_name):
+ rates_list = []
+ the_rates = open(rates_name)
+ for rate in the_rates.readlines():
+ rates_list.append([float(rate)])
+ rate_array = np.array(rates_list)
+ return rate_array
+
+_binary_name = 'fast_TIGER'
+if sys.platform == 'win32':
+ _binary_name += ".exe"
+_tiger_binary = None
+
+def run_rates(command):
+ global _tiger_binary
+ if _tiger_binary is None:
+ _tiger_binary = util.find_program(_binary_name)
+
+ try:
+ util.run_program(_tiger_binary, command)
+ except util.ExternalProgramError:
+ log.error("fast_TIGER did not execute successfully")
+ log.error("fast_TIGER output follows, in case it's helpful for \
+ finding the problem")
+ log.error("You probably just need to recompile the fast_TIGER \
+ code for your system. But please note that this is an \
+ unsupported option. For empirical work we recommend using \
+ entropy calculations for site rates, which is the default \
+ behaviour for the kmeans algorithm in PF2.")
+ raise
+
+
+def sitewise_tiger_rates(cfg, phylip_file):
+ if cfg.datatype == 'DNA':
+ command = " dna " + phylip_file
+ elif cfg.datatype == 'morphology':
+ command = " morphology " + phylip_file
+ run_rates(command)
+ rates_name = ("%s_r8s.txt" % phylip_file)
+ return rate_parser(rates_name)
+
+
+def get_per_site_stats(alignment, cfg, a_subset):
+ if cfg.kmeans == 'entropy':
+ sub_align = SubsetAlignment(alignment, a_subset)
+ return entropy.sitewise_entropies(sub_align)
+ elif cfg.kmeans == 'fast_tiger':
+ a_subset.make_alignment(cfg, alignment)
+ phylip_file = a_subset.alignment_path
+ return sitewise_tiger_rates(cfg, str(phylip_file))
+ elif cfg.kmeans == 'tiger':
+ sub_align = SubsetAlignment(alignment, a_subset)
+ tiger = the_config.TigerDNA()
+ tiger.build_bitsets(sub_align)
+ rate_array = tiger.calc_rates()
+ rate_array.shape = rate_array.shape[0], 1
+ return rate_array
+ else: #wtf
+ log.error("Unkown option passed to 'kmeans'. Please check and try again")
+ raise PartitionFinderError
+
+
+def kmeans_split_subset(cfg, alignment, a_subset, tree_path,
+ n_jobs, number_of_ks=2):
+ """Takes a subset and number of k's and returns
+ subsets for however many k's are specified
+ """
+ # Get either entropies or TIGER rates
+ per_site_stat_list = get_per_site_stats(alignment, cfg, a_subset)
+
+ # Now store all of the per_site_stats with the subset
+ a_subset.add_per_site_statistics(per_site_stat_list)
+ log.debug("The per site statistics for the first 10 sites of subset %s are %s"
+ % (a_subset.name, per_site_stat_list[0:10]))
+
+ # Perform kmeans clustering on the per site stats
+ kmeans_results = kmeans(per_site_stat_list, number_of_ks, n_jobs)
+ centroids = kmeans_results[0]
+ split_categories = kmeans_results[1]
+
+ list_of_sites = []
+ for k in range(len(split_categories)):
+ list_of_sites.append(split_categories[k])
+
+ log.debug("# split categories: %d" % len(split_categories))
+
+ log.debug("Creating new subsets from k-means split")
+ # Make the new subsets
+ new_subsets = subset_ops.split_subset(a_subset, list_of_sites)
+
+ # Now add the site_lnl centroid to each new subset
+ marker = 0
+ for s in new_subsets:
+ s.centroid = centroids[marker]
+ marker += 1
+
+ return new_subsets
diff --git a/partfinder/logtools.py b/partfinder/logtools.py
new file mode 100644
index 0000000..9b1406a
--- /dev/null
+++ b/partfinder/logtools.py
@@ -0,0 +1,160 @@
+import logging
+import os
+import re
+import textwrap
+import inspect
+
+_log_depth = 0
+_max_width = 80
+_tab_width = 2
+
+# These should be the same size as the _tab_width
+_bullet = ""
+_continuation = "..."
+
+def get_logger(fname=None):
+ """Pass in the __file__"""
+
+ # Magically get the filename from the calling function
+ if fname is None:
+ caller_frame = inspect.stack()[1][0]
+ fname = caller_frame.f_globals['__file__']
+
+ # Strip the beginning and the extension
+ head_tail = os.path.split(fname)
+ base_ext = os.path.splitext(head_tail[1])
+
+ log_name = base_ext[0]
+
+ # Trim it max 10 characters
+ log_name = log_name[:10]
+
+ # Now wrap it and return it
+ # return DumbLogger(logging.getLogger(log_name))
+ return SmartLogger(logging.getLogger(log_name))
+
+class DumbLogger(object):
+ def __init__(self, logger):
+ self.log = logger
+
+ def debug(self, *args):
+ self.log.debug(*args)
+
+ def info(self, *args):
+ self.log.info(*args)
+
+ def warning(self, *args):
+ self.log.warning(*args)
+
+ def error(self, *args):
+ self.log.error(*args)
+
+ def push():
+ pass
+
+ def pop():
+ pass
+
+
+class SmartLogger(object):
+ def __init__(self, logger):
+ self.log = logger
+
+ def debug(self, *args):
+ msg = self.compose_message(*args)
+ self.post_message(msg, self.log.debug)
+
+ def info(self, *args):
+ msg = self.compose_message(*args)
+ self.post_message(msg, self.log.info)
+
+ def warning(self, *args):
+ msg = self.compose_message(*args)
+ self.post_message(msg, self.log.warning)
+
+ def error(self, *args):
+ msg = self.compose_message(*args)
+ self.post_message(msg, self.log.error)
+
+ def format_message(self, msg):
+ """Strip multiline comments down to a single line"""
+ # First, get rid of tabs and newlines
+ warning = re.sub('\s', ' ', msg)
+
+ # Now get rid of all extra spaces
+ # http://stackoverflow.com/questions/1546226/
+ # the-shortest-way-to-remove-multiple-spaces-in-a-string-in-python
+ return ' '.join(warning.split())
+
+ def compose_message(self, *args):
+ if len(args) > 1:
+ msg = args[0] % args[1:]
+ else:
+ msg = args[0]
+ msg = self.format_message(msg)
+ return msg
+
+ def normal_post_message(self, msg, log_function):
+ indent_amount = _log_depth * (_tab_width + 1)
+ spaces = " " * indent_amount
+ log_function(spaces + msg)
+
+ def clever_post_message(self, msg, log_function):
+ # How much room have we got?
+ indent_amount = _log_depth * (_tab_width + 1)
+ local_max_width = _max_width - indent_amount
+ spaces = " " * indent_amount
+
+ # Note: if this happens, you're doing too much formatting. Get rid of
+ # some of the "push" calls
+ # TODO: you can't do an assert here.
+ assert local_max_width > 30
+
+ if len(msg) <= local_max_width:
+ log_function(spaces + _bullet + msg)
+ return
+
+ # Add an extra for the hanging indent
+ lines = textwrap.wrap(msg, local_max_width)
+ line_iterator = iter(lines)
+ first = line_iterator.next()
+ log_function(spaces + _bullet + first)
+ for next_line in line_iterator:
+ log_function(spaces + _continuation + next_line)
+
+ post_message = normal_post_message
+
+ def push(self):
+ global _log_depth
+ _log_depth += 1
+
+ def pop(self):
+ global _log_depth
+ _log_depth -= 1
+
+
+class indented(object):
+ def __init__(self, logger=None, msg=None):
+ self.logger = logger
+ self.msg = msg
+
+ def __enter__(self):
+ if self.logger and self.msg:
+ self.logger.info(self.msg)
+ self.logger.push()
+
+ def __exit__(self, type, value, traceback):
+ self.logger.pop()
+
+
+class log_info(object):
+ """Decorator for wrapping functions indented"""
+ def __init__(self, logger, msg):
+ self.logger = logger
+ self.msg = msg
+
+ def __call__(self, fn):
+ def indented_fn(*args, **kwargs):
+ with indented(self.logger, self.msg):
+ fn(*args, **kwargs)
+ return indented_fn
diff --git a/partfinder/main.py b/partfinder/main.py
new file mode 100644
index 0000000..de3307e
--- /dev/null
+++ b/partfinder/main.py
@@ -0,0 +1,429 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+__VERSION__ = "2.0.0"
+
+import logging
+import sys
+import shlex
+import logtools
+
+logging.basicConfig(
+ format="%(levelname)-8s | %(asctime)s | %(message)s",
+ level=logging.INFO
+)
+
+log = logtools.get_logger()
+from optparse import OptionParser
+
+# We import everything here as it forces all of debug regions to be loaded
+import config
+import analysis_method
+import util
+import reporter
+import progress
+import datetime
+import parser
+import raxml
+import phyml
+
+
+def debug_arg_callback(option, opt, value, theparser):
+ setattr(theparser.values, option.dest, value.split(','))
+
+
+def get_debug_regions():
+ mlogger = logging.Logger.manager
+ return mlogger.loggerDict.keys()
+
+
+def set_debug_regions(regions):
+ if regions is None:
+ return
+ valid_regions = set(get_debug_regions())
+ if 'all' in regions:
+ regions = valid_regions
+ else:
+ regions = set(regions)
+ errors = set()
+ for r in regions:
+ if r not in valid_regions:
+ log.error("'%s' is not a valid debug region", r)
+ errors.add(r)
+ if errors:
+ return errors
+
+ for r in regions:
+ logging.getLogger(r).setLevel(logging.DEBUG)
+
+ # Enhance the format
+ fmt = logging.Formatter(
+ "%(levelname)-8s | %(asctime)s | %(name)-10s | %(message)s")
+ logging.getLogger("").handlers[0].setFormatter(fmt)
+
+ return None
+
+def parse_args(datatype, cmdargs=None):
+ usage = """usage: python %prog [options] <foldername>
+
+ PartitionFinder and PartitionFinderProtein are designed to discover optimal
+ partitioning schemes for nucleotide and amino acid sequence alignments.
+ They are also useful for finding the best model of sequence evolution for datasets.
+
+ The Input: <foldername>: the full path to a folder containing:
+ - A configuration file (partition_finder.cfg)
+ - A nucleotide/aa alignment in Phylip format
+ Take a look at the included 'example' folder for more details.
+
+ The Output: A file in the same directory as the .cfg file, named
+ 'analysis' This file contains information on the best
+ partitioning scheme, and the best model for each partiiton
+
+ Usage Examples:
+ >python %prog example
+ Analyse what is in the 'example' sub-folder in the current folder.
+
+ >python %prog -v example
+ Analyse what is in the 'example' sub-folder in the current folder, but
+ show all the debug output
+
+ >python %prog -c ~/data/frogs
+ Check the configuration files in the folder data/frogs in the current
+ user's home folder.
+
+ >python %prog --force-restart ~/data/frogs
+ Deletes any data produced by the previous runs (which is in
+ ~/data/frogs/output) and starts afresh
+ """
+ op = OptionParser(usage)
+ op.add_option(
+ "-v", "--verbose",
+ action="store_true", dest="verbose",
+ help="show debug logging information (equivalent to --debug-out=all)")
+ op.add_option(
+ "-c", "--check-only",
+ action="store_true", dest="check_only",
+ help="just check the configuration files, don't do any processing")
+ op.add_option(
+ "-f", "--force-restart",
+ action="store_true", dest="force_restart",
+ help="delete all previous output and start afresh (!)")
+ op.add_option(
+ "-p", "--processes",
+ type="int", dest="processes", default=-1, metavar="N",
+ help="Number of concurrent processes to use."
+ " Use -1 to match the number of cpus on the machine."
+ " The default is to use -1.")
+ op.add_option(
+ "--show-python-exceptions",
+ action="store_true", dest="show_python_exceptions",
+ help="If errors occur, print the python exceptions")
+ op.add_option(
+ "--save-phylofiles",
+ action="store_true", dest="save_phylofiles",
+ help="save all of the phyml or raxml output. This can take a lot of space(!)")
+ op.add_option(
+ "--dump-results",
+ action="store_true", dest="dump_results",
+ help="Dump all results to a binary file. "
+ "This is only of use for testing purposes.")
+ op.add_option(
+ "--compare-results",
+ action="store_true", dest="compare_results",
+ help="Compare the results to previously dumped binary results. "
+ "This is only of use for testing purposes.")
+ op.add_option(
+ "-q", "--quick",
+ action="store_true", dest="quick", default=False,
+ help="Avoid anything slow (like writing schemes at each step),"
+ "useful for very large datasets."
+ )
+ op.add_option(
+ "-r", "--raxml",
+ action="store_true", dest="raxml",
+ help="Use RAxML (rather than PhyML) to do the analysis. See the manual"
+ )
+ op.add_option(
+ "--cmdline-extras",
+ type="str", dest="cmdline_extras", default="", metavar="N",
+ help="Add additional commands to the phyml or raxml commandlines that PF uses."
+ "This can be useful e.g. if you want to change the accuracy of lnL calculations"
+ " ('-e' option in raxml), or use multi-threaded versions of raxml that require"
+ " you to specify the number of threads you will let raxml use ('-T' option in "
+ "raxml. E.g. you might specify this: --cmndline_extras ' -e 2.0 -T 10 '"
+ " N.B. MAKE SURE YOU PUT YOUR EXTRAS IN QUOTES, and only use this command if you"
+ " really know what you're doing and are very familiar with raxml and"
+ " PartitionFinder"
+ )
+ op.add_option(
+ "--weights",
+ type="str", dest="cluster_weights", default=None, metavar="N",
+ help="Mainly for algorithm development. Only use it if you know what you're doing."
+ "A list of weights to use in the clustering algorithms. This list allows you "
+ "to assign different weights to: the overall rate for a subset, the base/amino acid "
+ "frequencies, model parameters, and alpha value. This will affect how subsets are "
+ "clustered together. For instance: --cluster_weights '1, 2, 5, 1', would weight "
+ "the base freqeuncies 2x more than the overall rate, the model parameters 5x "
+ "more, and the alpha parameter the same as the model rate"
+ )
+ op.add_option(
+ "--kmeans",
+ type="str", dest="kmeans", default='entropy', metavar="type",
+ help="This defines which sitewise values to use: entropy or tiger"
+ "\n--kmeans entropy: use entropies for sitewise values"
+ "\n--kmeans tiger: use TIGER rates for sitewise values"
+ )
+ op.add_option(
+ "--rcluster-percent",
+ type="float", dest="cluster_percent", default=10.0, metavar="N",
+ help="This defines the proportion of possible schemes that the relaxed clustering"
+ " algorithm will consider before it stops looking. The default is 10%."
+ "e.g. --rcluster-percent 10.0"
+ )
+ op.add_option(
+ "--rcluster-max",
+ type="int", dest="cluster_max", default=1000, metavar="N",
+ help="This defines the number of possible schemes that the relaxed clustering"
+ " algorithm will consider before it stops looking. The default is to look at "
+ "just the top 1000 schemes."
+ "e.g. --rcluster-max 1000"
+ )
+ op.add_option(
+ "--min-subset-size",
+ type="int", dest="min_subset_size", default=100, metavar="N",
+ help="This defines the minimum subset size that you will accept for"
+ " the kmeans algorithm. Subsets smaller than this will still be "
+ "created during the algorithm, but they will be merged with other"
+ " subsets at the end of the algorithm."
+ "e.g. --min-subset-size 100"
+ )
+ op.add_option(
+ '--debug-output',
+ type='string',
+ action='callback',
+ dest='debug_output',
+ metavar="REGION,REGION,...",
+ callback=debug_arg_callback,
+ help="(advanced option) Provide a list of debug regions to output extra "
+ "information about what the program is doing."
+ " Possible regions are 'all' or any of {%s}."
+ % ",".join(get_debug_regions())
+ )
+ op.add_option(
+ "--all-states",
+ action="store_true", dest="all_states", default=False,
+ help="In the k-means algorithm, only produce subsets which have "
+ "all states represented (e.g. ACTG for DNA datasets)."
+ )
+
+ op.add_option(
+ '--profile',
+ action="store_true",
+ help="Output profiling information after running (this will slow everything down!)")
+
+ if cmdargs is None:
+ options, args = op.parse_args()
+ else:
+ options, args = op.parse_args(cmdargs)
+
+ options.datatype = datatype
+ # We should have one argument: the folder to read the configuration from
+ if not args:
+ op.print_help()
+ else:
+ check_options(op, options)
+
+ return options, args
+
+
+def check_options(op, options):
+ # Error checking
+ if options.dump_results and options.compare_results:
+ op.error(
+ "options --dump_results and --compare_results are mutually exclusive!")
+
+ if options.verbose:
+ set_debug_regions(['all'])
+ else:
+ errors = set_debug_regions(options.debug_output)
+ if errors is not None:
+ bad = ",".join(list(errors))
+ op.error("Invalid debug regions: %s" % bad)
+
+ # Default to phyml
+ if options.raxml == 1:
+ options.phylogeny_program = 'raxml'
+ else:
+ options.phylogeny_program = 'phyml'
+
+ #A warning for people using the Pthreads version of RAxML
+ if options.cmdline_extras.count("-T") > 0:
+ log.warning("""
+ It looks like you're using a Pthreads version of RAxML. Be aware
+ that the default behaviour of PartitionFinder is to run one version
+ of RAxML per available processor. This might not be what you want
+ with Pthreads, since the minimum number of threads per RAxML run is
+ 2 (i.e. -T 2). Make sure to limit the total number of RAxML runs
+ you start using the -p option in PartitionFinder. Specifically,
+ the total number of processors you will use with the Pthreads
+ version is the number you set via the -T option in
+ --cmdline-extras, multiplied by the number of processors you set
+ via the -p option in PartitionFinder. You should also be aware
+ that the Pthreads version of RAxML has a rare but known bug on some
+ platforms. This bug results in infinite likelihood values if it
+ happens on your dataset, PartitionFinder will give an error. In
+ that case you should switch back to using a single-threaded version
+ of RAxML, e.g. the SSE3 or AVX version. See the manual for more
+ info.""")
+
+
+def check_python_version():
+ """Check the python version is above 2.7 but lower than 3.0"""
+
+ python_version = float(
+ "%d.%d" % (sys.version_info[0], sys.version_info[1]))
+
+ log.info("You have Python version %.1f" % python_version)
+
+ if python_version < 2.7:
+ log.error("""
+ Your Python version is %.1f, but this program requires Python 2.7.
+ Please upgrade to version 2.7 by visiting www.python.org/getit,
+ or by following the instructions in the PartitionFinder manual.
+ """ % python_version)
+ return 0
+
+ if python_version > 3.0:
+ log.warning("""
+ Your Python version is %.1f. This program was not built to run
+ with version 3 or higher. To guarantee success, please use
+ Python 2.7.x""" % python_version)
+
+def run_analysis(cfg, options):
+ # Now try processing everything....
+ method = analysis_method.choose_method(cfg.search)
+ reporter.TextReporter(cfg)
+ anal = method(cfg, options.force_restart, options.processes)
+ results = anal.analyse()
+ if options.dump_results:
+ results.dump(cfg)
+ elif options.compare_results:
+ results.compare(cfg)
+
+def profile_analysis(cfg, options):
+ import cProfile, pstats
+ cProfile.runctx('run_analysis(cfg, options)', globals(), locals(), filename='profile.output')
+ p = pstats.Stats('profile.output')
+ p.sort_stats('time').print_stats(20)
+ p.sort_stats('cumtime').print_stats(20)
+ # p.strip_dirs().sort_stats(-1).print_stats()
+
+def main(name, datatype, passed_args=None):
+
+ # If passed_args is None, this will use sys.argv
+ options, args = parse_args(datatype, passed_args)
+ if not args:
+ # Help has already been printed
+ return 2
+
+ log.info("------------- %s %s -----------------" % (name, __VERSION__))
+ start_time = datetime.datetime.now().replace(
+ microsecond=0) # start the clock ticking
+
+ check_python_version()
+
+ if passed_args is None:
+ cmdline = " ".join(sys.argv)
+ else:
+ cmdline = " ".join(passed_args)
+
+ log.info("Command-line arguments used: %s" % cmdline)
+
+ # Load, using the first argument as the folder
+ try:
+ # TODO: just pass the options in!
+ config.the_config.init(datatype,
+ options.phylogeny_program,
+ options.save_phylofiles,
+ options.cmdline_extras,
+ options.cluster_weights,
+ options.cluster_percent,
+ options.cluster_max,
+ options.kmeans,
+ options.quick,
+ options.min_subset_size,
+ options.all_states)
+ cfg = config.the_config
+
+ # Set up the progress callback
+ progress.TextProgress(cfg)
+ cfg.load_base_path(args[0])
+
+ if options.check_only:
+ log.info("""
+ Exiting without processing (because of the
+ -c/--check-only option ...
+ """)
+ else:
+ try:
+ if options.profile:
+ profile_analysis(cfg, options)
+ else:
+ run_analysis(cfg, options)
+ finally:
+ # Make sure that we reset the configuration
+ cfg.reset()
+
+ # Successful exit
+ end_time = datetime.datetime.now().replace(microsecond=0)
+ processing_time = end_time - start_time
+
+ log.info("Total processing time: %s (h:m:s)" % processing_time)
+ log.info("Processing complete.")
+
+ return 0
+
+ except util.ExternalProgramError as e:
+ log.error("""A program that Partitionfinder uses failed. Output
+ follows, in case it's helpful for finding the problem""")
+ log.error("%s", e.stdout)
+ log.error("%s", e.stderr)
+ if options.show_python_exceptions or passed_args is not None:
+ raise
+
+ except util.ParseError:
+ log.error("""We failed to parse the output of an external program (See
+ previous errors). This is probably due to an update to the
+ program which has changed the output.""")
+ if options.show_python_exceptions or passed_args is not None:
+ raise
+
+ except util.PartitionFinderError:
+ log.error("Failed to run. See previous errors.")
+ # Reraise if we were called by call_main, or if the options is set
+ if options.show_python_exceptions or passed_args is not None:
+ raise
+
+ except (KeyboardInterrupt, SystemExit):
+ log.error("User interrupted the Program")
+
+ return 1
+
+
+def call_main(datatype, cmdline):
+ cmdargs = shlex.split(cmdline)
+ main("<main.py:call_main(%s)>" % datatype, datatype, cmdargs)
diff --git a/partfinder/model_loader.py b/partfinder/model_loader.py
new file mode 100644
index 0000000..a4dc0c6
--- /dev/null
+++ b/partfinder/model_loader.py
@@ -0,0 +1,181 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+import pandas as pd
+import os
+import collections
+
+log = logtools.get_logger()
+from util import PartitionFinderError
+
+_available_lists = ["ALL", # all models, excluding those with base frequencies estimated by ML and protein GTR models
+ "ALLX", # all models, including those with base frequencies estimated by ML and protein GTR models
+ "BEAST", # all models available in BEAST 2
+ "MRBAYES", # all models available in MrBayes 3.3
+ "GAMMA", # only models with gamma distributed rates only (i.e. +G, not +I+G, not free-rates models like LG4X)
+ "GAMMAI", # only modles with +I+G
+ ]
+
+
+def load_models(the_config):
+ HERE = os.path.abspath(os.path.dirname(__file__))
+ the_config.all_models = pd.read_csv(os.path.join(HERE, 'models.csv'))
+
+ # determine available models based on datatype and phylogeny program
+ the_config.available_models = get_available_models(the_config)
+
+ # check user models will run
+ parse_user_models(the_config)
+
+ log.info("This analysis will use the following %d models of molecular evolution"
+ % len(the_config.models))
+ log.info("%s" % ', '.join(the_config.models))
+
+
+def get_available_models(the_config):
+ # from the list of all models, which ones could we actually run
+ if the_config.phylogeny_program == 'phyml':
+ available_models = the_config.all_models[pd.notnull(the_config.all_models.phyml_commandline)]
+ elif the_config.phylogeny_program == 'raxml':
+ available_models = the_config.all_models[pd.notnull(the_config.all_models.raxml_commandline)]
+
+ if the_config.datatype == 'DNA':
+ available_models = available_models.query("datatype=='DNA'")
+ elif the_config.datatype == 'protein':
+ available_models = available_models.query("datatype=='protein'")
+ elif the_config.datatype == 'morphology':
+ available_models = available_models.query("datatype=='morphology'")
+ else:
+ log.error("Unknown datatype '%s'" % the_config.datatype)
+
+ if len(available_models) == 0:
+ log.error("""Phylogeny program '%s' does not implement any models that deal
+ with %s data. Please check and try again. For morphological data,
+ use RAxML (--raxml at the commandline)""" %
+ (the_config.phylogeny_program, the_config.datatype))
+ raise PartitionFinderError
+
+ return available_models
+
+def parse_user_models(the_config):
+
+ # this will tell us if they entered any lists or models we can't use
+ check_all_models_and_lists(the_config)
+
+ check_for_duplicates(the_config.models)
+
+ mod_list = check_model_lists(the_config.models)
+
+ if mod_list:
+ expand_model_list(the_config)
+
+ # final check on models
+ check_all_models(the_config)
+
+def check_all_models(the_config):
+ # everything has to be a model in the_config.available_models
+ models = the_config.models
+ allowed = set(the_config.available_models.name)
+
+
+ problems = set(models).difference(allowed)
+
+ if problems:
+ log.error("""'%s' is/are not a valid model(s) for phylogeny program %s
+ and data type %s, please check and try again"""
+ %(', '.join(problems), the_config.phylogeny_program, the_config.datatype))
+ log.info("""If you are unsure which models are available, or why a model you think
+ should work does not, please check the manual and the models.csv file
+ (located in the /partfinder folder) for more information.""")
+ raise PartitionFinderError
+
+def check_all_models_and_lists(the_config):
+ # everything has to be either a model in the_config.available_models
+ # OR a valid option from the _available_models
+ models = the_config.models
+ allowed = set(_available_lists).union(set(the_config.available_models.name))
+
+ allmods = set(_available_lists).union(set(the_config.all_models.name))
+
+ # first we check for stuff that's not anywhere on our lists
+ mistakes = set(models).difference(allmods)
+
+ if mistakes:
+ if len(mistakes)>1: t = 'are not models/lists that are'
+ else: t = 'is not a model/list that is'
+
+ log.error("""'%s' %s implemented in PartitionFinder. Perhaps
+ you made a mistake. Please check and try again"""
+ %(', '.join(mistakes), t))
+ log.info("""If you are unsure which models are available, or why a model you think
+ should work does not, please check the manual and the models.csv file
+ (located in the /partfinder folder) for more information.""")
+ raise PartitionFinderError
+
+
+ problems = set(models).difference(allowed)
+
+ if problems:
+ log.error("""'%s' is/are not a valid model(s) or lists of models
+ for phylogeny program %s and data type %s,
+ please check and try again."""
+ %(', '.join(problems), the_config.phylogeny_program, the_config.datatype))
+
+ log.info("""If you are unsure which models are available, or why a model you think
+ should work does not, please check the manual and the models.csv file
+ (located in the /partfinder folder) for more information.""")
+ raise PartitionFinderError
+
+
+def check_model_lists(models):
+
+ mod_lists = set(models).intersection(set(_available_lists))
+
+ if mod_lists and len(models)>1:
+ log.error("""If you use a model list (you used '%s') you can only
+ specify a single list, and no other lists or models. Please
+ check and try again.""" % ', '.join(mod_lists))
+ raise PartitionFinderError
+
+ return mod_lists
+
+
+def expand_model_list(the_config):
+
+ # by this point, we know that mod_list is a list of length 1
+ mod_list = the_config.models[0]
+
+ the_config.models = list(the_config.available_models.query("%s==1" % mod_list).name)
+
+ if len(the_config.models)<1:
+ log.error("""The model list '%s' is not a compatible with
+ for phylogeny program %s and data type %s.
+ There are no models in that list which work with
+ that combination of program and data type. Please check and try again."""
+ %(mod_list, the_config.phylogeny_program, the_config.datatype))
+ raise PartitionFinderError
+
+
+def check_for_duplicates(models):
+ # model lists shouldn't contain duplicated models
+ duplicates = [x for x, y in collections.Counter(models).items() if y > 1]
+ if len(duplicates)>0:
+ log.error("""There was a problem loading your list of models,
+ the following models seem to be duplicated: %s"""
+ % duplicates)
+ raise PartitionFinderError
diff --git a/partfinder/model_utils.py b/partfinder/model_utils.py
new file mode 100644
index 0000000..0c9e7d2
--- /dev/null
+++ b/partfinder/model_utils.py
@@ -0,0 +1,65 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+import pandas as pd
+import os
+from config import the_config
+
+log = logtools.get_logger()
+from util import PartitionFinderError
+
+def get_num_params(modelstring):
+ """
+ Input a model string like HKY+I+G or LG+G+F, and get the number of
+ parameters
+ """
+
+ m = the_config.available_models.query("name=='%s'" %modelstring).matrix_params.values[0]
+ b = the_config.available_models.query("name=='%s'" %modelstring).basefreq_params.values[0]
+ r = the_config.available_models.query("name=='%s'" %modelstring).ratevar_params.values[0]
+
+ total = m+b+r
+
+ log.debug("Model: %s Params: %d" % (modelstring, total))
+
+ return total
+
+def get_raxml_protein_modelstring(modelstring):
+ """Start with a model like this: LG+I+G+F, return a model in raxml format like this:
+ LGF. This is only used for printing out RAxML partition files
+ NB. In RAxML you can't specify different rate hetero parameters in each protein model
+ you have to choose either ALL +G or ALL +I+G. PartitionFinder allows you to mix and
+ match here, but if you're going to use RAxML downstream, you will need to be smarter
+ and run two analyses - one with just +I+G models, and one with +G models.
+
+ So really all we do is add an F/X to the model name if it used +F.
+ """
+
+ elements = modelstring.split("+")
+ model_name = elements[0]
+ extras = elements[1:]
+
+ raxmlstring = model_name
+ if "F" in extras:
+ raxmlstring = ''.join([raxmlstring, "F"])
+ elif "X" in extras:
+ raxmlstring = ''.join([raxmlstring, "X"])
+
+ return raxmlstring
+
+
diff --git a/partfinder/models.csv b/partfinder/models.csv
new file mode 100644
index 0000000..788d3b2
--- /dev/null
+++ b/partfinder/models.csv
@@ -0,0 +1 @@
+id,name,base_frequencies,rate_variation,matrix_params,basefreq_params,ratevar_params,datatype,phyml_commandline,raxml_commandline,notes,ALL,ALLX,BEAST,MRBAYES,GAMMA,GAMMAI,
1,JC,equal,none,0,0,0,DNA," -o lr -m 000000 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,1,1,0,0,
2,K80,equal,none,1,0,0,DNA," -o lr -m 010010 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,1,1,0,0,
3,TRNEF,equal,none,2,0,0,DNA," -o lr -m 010020 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,1,0,0,0,
4,K81,equal,none,2,0,0,DNA," -o lr -m 012210 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,0,0,0,0,
5,TVMEF,equal,none,4,0,0,DNA," -o lr -m 012314 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,0,0,0,0,
6,TIMEF,equal,none,3,0,0,DNA," -o lr -m 012230 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,0,0,0,0,
7,SYM,equal,none,5,0,0,DNA," -o lr -m 012345 -f '0.25, 0.25, 0.25, 0.25' -c 1",NA,,1,1,1,1,0,0,
8,F81,empirical,none,0,3,0,DNA, -o lr -m 000000 -f e -c 1,NA,,1,1,0,1,0,0,
9,HKY,empirical,none,1,3,0,DNA, -o lr -m 010010 -f e -c 1,NA,,1,1,1,1,0,0,
10,TRN,empirical,none,2,3,0,DNA, -o lr -m 010020 -f e -c 1,NA,,1,1,1,0,0,0,
11,K81UF,empirical,none,2,3,0,DNA, -o lr -m 012210 -f e -c 1,NA,,1,1,0,0,0,0,
12,TVM,empirical,none,4,3,0,DNA, -o lr -m 012314 -f e -c 1,NA,,1,1,0,0,0,0,
13,TIM,empirical,none,3,3,0,DNA, -o lr -m 012230 -f e -c 1,NA,,1,1,0,0,0,0,
14,GTR,empirical,none,5,3,0,DNA, -o lr -m 012345 -f e -c 1, -m GTRCAT -V,,1,1,1,1,0,0,
15,F81+X,ML,none,0,3,0,DNA, -o lr -m 000000 -f m -c 1,NA,,0,1,0,0,0,0,
16,HKY+X,ML,none,1,3,0,DNA, -o lr -m 010010 -f m -c 1,NA,,0,1,1,0,0,0,
17,TRN+X,ML,none,2,3,0,DNA, -o lr -m 010020 -f m -c 1,NA,,0,1,1,0,0,0,
18,K81UF+X,ML,none,2,3,0,DNA, -o lr -m 012210 -f m -c 1,NA,,0,1,0,0,0,0,
19,TVM+X,ML,none,4,3,0,DNA, -o lr -m 012314 -f m -c 1,NA,,0,1,0,0,0,0,
20,TIM+X,ML,none,3,3,0,DNA, -o lr -m 012230 -f m -c 1,NA,,0,1,0,0,0,0,
21,GTR+X,ML,none,5,3,0,DNA, -o lr -m 012345 -f m -c 1, -m GTRCATX -V,,0,1,1,0,0,0,
22,LG,model,none,0,0,0,protein, -o lr -m LG -d aa -f m -c 1, -m PROTCATLG -V,,1,1,0,0,0,0,
23,WAG,model,none,0,0,0,protein, -o lr -m WAG -d aa -f m -c 1, -m PROTCATWAG -V,,1,1,1,1,0,0,
24,MTREV,model,none,0,0,0,protein, -o lr -m mtREV -d aa -f m -c 1, -m PROTCATMTREV -V,,1,1,1,1,0,0,
25,DAYHOFF,model,none,0,0,0,protein, -o lr -m Dayhoff -d aa -f m -c 1, -m PROTCATDAYHOFF -V,,1,1,1,1,0,0,
26,DCMUT,model,none,0,0,0,protein, -o lr -m DCMut -d aa -f m -c 1, -m PROTCATDCMUT -V,,1,1,0,0,0,0,
27,JTT,model,none,0,0,0,protein, -o lr -m JTT -d aa -f m -c 1, -m PROTCATJTT -V,,1,1,1,0,0,0,
28,VT,model,none,0,0,0,protein, -o lr -m VT -d aa -f m -c 1, -m PROTCATVT -V,,1,1,0,1,0,0,
29,BLOSUM62,model,none,0,0,0,protein, -o lr -m Blosum62 -d aa -f m -c 1, -m PROTCATBLOSUM62 -V,,1,1,1,1,0,0,
30,CPREV,model,none,0,0,0,protein, -o lr -m CpREV -d aa -f m -c 1, -m PROTCATCPREV -V,,1,1,1,1,0,0,
31,RTREV,model,none,0,0,0,protein, -o lr -m RtREV -d aa -f m -c 1, -m PROTCATRTREV -V,,1,1,0,1,0,0,
32,MTMAM,model,none,0,0,0,protein, -o lr -m MtMam -d aa -f m -c 1, -m PROTCATMTMAM -V,,1,1,0,1,0,0,
33,MTART,model,none,0,0,0,protein, -o lr -m MtArt -d aa -f m -c 1, -m PROTCATMTART -V,,1,1,0,0,0,0,
34,HIVB,model,none,0,0,0,protein, -o lr -m HIVb -d aa -f m -c 1, -m PROTCATHIVB -V,,1,1,0,0,0,0,
35,HIVW,model,none,0,0,0,protein, -o lr -m HIVw -d aa -f m -c 1, -m PROTCATHIVW -V,,1,1,0,0,0,0,
36,LG4M,model,none,0,0,0,protein,NA,NA,"LG4M has gamma rates by design. Thus, it doesn't make much sense to use it without them.",0,0,0,0,0,0,
37,LG4X,model,free,3,0,3,protein,NA, -m PROTGAMMALG4X,"Note that the LG4X model has 4 independent rate categories. So, it is nonsensical to try and estimate an LG4X model without any among-site rate variation. As a result, there is no entry in this file for the LG4X model without rate variation (i.e. with 'none' in the rate variation column). In fact, that model is just the LG model on line 22. So, for clarity the LG4X model is included here. Note that the fact that the call in RAxML star [...]
38,MTZOA,model,none,0,0,0,protein,NA, -m PROTCATMTZOA -V,,1,1,0,0,0,0,
39,PMB,model,none,0,0,0,protein,NA, -m PROTCATPMB -V,,1,1,0,0,0,0,
40,JTTDCMUT,model,none,0,0,0,protein,NA, -m PROTCATJTTDCMUT -V,,1,1,0,0,0,0,
41,FLU,model,none,0,0,0,protein,NA, -m PROTCATFLU -V,,1,1,0,0,0,0,
42,STMTREV,model,none,0,0,0,protein,NA, -m PROTCATSTMTREV -V,,1,1,0,0,0,0,
43,DUMMY,model,none,0,0,0,protein,NA, -m PROTCATDUMMY -V,,1,1,0,0,0,0,
44,DUMMY2,model,none,0,0,0,protein,NA, -m PROTCATDUMMY2 -V,,1,1,0,0,0,0,
45,GTR,model,none,189,0,0,protein,NA,NA,"Not possible, because by definition the GTR model does not have any amino acid frequencies with it. So they either need to be estimated from the data empirically (see GTR+F) or by ML (not implemented in RAxML or, therefore, PartitionFinder).",0,0,0,0,0,0,
46,LG+F,empirical,none,0,19,0,protein, -o lr -m LG -d aa -f e -c 1, -m PROTCATLG -V,,1,1,0,0,0,0,
47,WAG+F,empirical,none,0,19,0,protein, -o lr -m WAG -d aa -f e -c 1, -m PROTCATWAG -V,,1,1,0,1,0,0,
48,MTREV+F,empirical,none,0,19,0,protein, -o lr -m mtREV -d aa -f e -c 1, -m PROTCATMTREV -V,,1,1,0,1,0,0,
49,DAYHOFF+F,empirical,none,0,19,0,protein, -o lr -m Dayhoff -d aa -f e -c 1, -m PROTCATDAYHOFF -V,,1,1,0,1,0,0,
50,DCMUT+F,empirical,none,0,19,0,protein, -o lr -m DCMut -d aa -f e -c 1, -m PROTCATDCMUT -V,,1,1,0,0,0,0,
51,JTT+F,empirical,none,0,19,0,protein, -o lr -m JTT -d aa -f e -c 1, -m PROTCATJTT -V,,1,1,0,0,0,0,
52,VT+F,empirical,none,0,19,0,protein, -o lr -m VT -d aa -f e -c 1, -m PROTCATVT -V,,1,1,0,1,0,0,
53,BLOSUM62+F,empirical,none,0,19,0,protein, -o lr -m Blosum62 -d aa -f e -c 1, -m PROTCATBLOSUM62 -V,,1,1,0,1,0,0,
54,CPREV+F,empirical,none,0,19,0,protein, -o lr -m CpREV -d aa -f e -c 1, -m PROTCATCPREV -V,,1,1,0,1,0,0,
55,RTREV+F,empirical,none,0,19,0,protein, -o lr -m RtREV -d aa -f e -c 1, -m PROTCATRTREV -V,,1,1,0,1,0,0,
56,MTMAM+F,empirical,none,0,19,0,protein, -o lr -m MtMam -d aa -f e -c 1, -m PROTCATMTMAM -V,,1,1,0,1,0,0,
57,MTART+F,empirical,none,0,19,0,protein, -o lr -m MtArt -d aa -f e -c 1, -m PROTCATMTART -V,,1,1,0,0,0,0,
58,HIVB+F,empirical,none,0,19,0,protein, -o lr -m HIVb -d aa -f e -c 1, -m PROTCATHIVB -V,,1,1,0,0,0,0,
59,HIVW+F,empirical,none,0,19,0,protein, -o lr -m HIVw -d aa -f e -c 1, -m PROTCATHIVW -V,,1,1,0,0,0,0,
60,LG4M+F,empirical,none,0,19,0,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
61,LG4X+F,empirical,none,6,19,0,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
62,MTZOA+F,empirical,none,0,19,0,protein,NA, -m PROTCATMTZOA -V,,1,1,0,0,0,0,
63,PMB+F,empirical,none,0,19,0,protein,NA, -m PROTCATPMB -V,,1,1,0,0,0,0,
64,JTTDCMUT+F,empirical,none,0,19,0,protein,NA, -m PROTCATJTTDCMUT -V,,1,1,0,0,0,0,
65,FLU+F,empirical,none,0,19,0,protein,NA, -m PROTCATFLU -V,,1,1,0,0,0,0,
66,STMTREV+F,empirical,none,0,19,0,protein,NA, -m PROTCATSTMTREV -V,,1,1,0,0,0,0,
67,DUMMY+F,empirical,none,0,19,0,protein,NA, -m PROTCATDUMMY -V,,1,1,0,0,0,0,
68,DUMMY2+F,empirical,none,0,19,0,protein,NA, -m PROTCATDUMMY2 -V,,1,1,0,0,0,0,
69,GTR+F,empirical,none,189,19,0,protein,NA,NA,,0,0,0,1,0,0,
70,LG+X,ML,none,0,19,0,protein,NA, -m PROTGAMMALGX,,0,1,0,0,0,0,
71,WAG+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAWAGX,,0,1,0,0,0,0,
72,MTREV+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAMTREVX,,0,1,0,0,0,0,
73,DAYHOFF+X,ML,none,0,19,0,protein,NA, -m PROTGAMMADAYHOFFX,,0,1,0,0,0,0,
74,DCMUT+X,ML,none,0,19,0,protein,NA, -m PROTGAMMADCMUTX,,0,1,0,0,0,0,
75,JTT+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAJTTX,,0,1,0,0,0,0,
76,VT+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAVTX,,0,1,0,0,0,0,
77,BLOSUM62+X,ML,none,0,19,0,protein,NA, -m PROTGAMMABLOSUM62X,,0,1,0,0,0,0,
78,CPREV+X,ML,none,0,19,0,protein,NA, -m PROTGAMMACPREVX,,0,1,0,0,0,0,
79,RTREV+X,ML,none,0,19,0,protein,NA, -m PROTGAMMARTREVX,,0,1,0,0,0,0,
80,MTMAM+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAMTMAMX,,0,1,0,0,0,0,
81,MTART+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAMTARTX,,0,1,0,0,0,0,
82,HIVB+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAHIVBX,,0,1,0,0,0,0,
83,HIVW+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAHIVWX,,0,1,0,0,0,0,
84,LG4M+X,ML,none,0,19,0,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
85,LG4X+X,ML,none,6,19,0,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
86,MTZOA+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAMTZOAX,,0,1,0,0,0,0,
87,PMB+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAPMBX,,0,1,0,0,0,0,
88,JTTDCMUT+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAJTTDCMUTX,,0,1,0,0,0,0,
89,FLU+X,ML,none,0,19,0,protein,NA, -m PROTGAMMAFLUX,,0,1,0,0,0,0,
90,STMTREV+X,ML,none,0,19,0,protein,NA, -m PROTGAMMASTMTREVX,,0,1,0,0,0,0,
91,DUMMY+X,ML,none,0,19,0,protein,NA, -m PROTGAMMADUMMYX,,0,1,0,0,0,0,
92,DUMMY2+X,ML,none,0,19,0,protein,NA, -m PROTGAMMADUMMY2X,,0,1,0,0,0,0,
93,GTR+X,ML,none,189,19,0,protein,NA,NA,"Possible in theory, but not implemented in RAxML and therefore not implemented in PF",0,0,0,0,0,0,
94,JC+G,equal,gamma,0,0,1,DNA," -o lr -m 000000 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,1,1,1,0,
95,K80+G,equal,gamma,1,0,1,DNA," -o lr -m 010010 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,1,1,1,0,
96,TRNEF+G,equal,gamma,2,0,1,DNA," -o lr -m 010020 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,1,0,1,0,
97,K81+G,equal,gamma,2,0,1,DNA," -o lr -m 012210 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,0,0,1,0,
98,TVMEF+G,equal,gamma,4,0,1,DNA," -o lr -m 012314 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,0,0,1,0,
99,TIMEF+G,equal,gamma,3,0,1,DNA," -o lr -m 012230 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,0,0,1,0,
100,SYM+G,equal,gamma,5,0,1,DNA," -o lr -m 012345 -f '0.25, 0.25, 0.25, 0.25' -a e -c 4",NA,,1,1,1,1,1,0,
101,F81+G,empirical,gamma,0,3,1,DNA, -o lr -m 000000 -f e -a e -c 4,NA,,1,1,0,1,1,0,
102,HKY+G,empirical,gamma,1,3,1,DNA, -o lr -m 010010 -f e -a e -c 4,NA,,1,1,1,1,1,0,
103,TRN+G,empirical,gamma,2,3,1,DNA, -o lr -m 010020 -f e -a e -c 4,NA,,1,1,1,0,1,0,
104,K81UF+G,empirical,gamma,2,3,1,DNA, -o lr -m 012210 -f e -a e -c 4,NA,,1,1,0,0,1,0,
105,TVM+G,empirical,gamma,4,3,1,DNA, -o lr -m 012314 -f e -a e -c 4,NA,,1,1,0,0,1,0,
106,TIM+G,empirical,gamma,3,3,1,DNA, -o lr -m 012230 -f e -a e -c 4,NA,,1,1,0,0,1,0,
107,GTR+G,empirical,gamma,5,3,1,DNA, -o lr -m 012345 -f e -a e -c 4, -m GTRGAMMA,,1,1,1,1,1,0,
108,F81+G+X,ML,gamma,0,3,1,DNA, -o lr -m 000000 -f m -a e -c 4,NA,,0,1,0,0,0,0,
109,HKY+G+X,ML,gamma,1,3,1,DNA, -o lr -m 010010 -f m -a e -c 4,NA,,0,1,1,0,0,0,
110,TRN+G+X,ML,gamma,2,3,1,DNA, -o lr -m 010020 -f m -a e -c 4,NA,,0,1,1,0,0,0,
111,K81UF+G+X,ML,gamma,2,3,1,DNA, -o lr -m 012210 -f m -a e -c 4,NA,,0,1,0,0,0,0,
112,TVM+G+X,ML,gamma,4,3,1,DNA, -o lr -m 012314 -f m -a e -c 4,NA,,0,1,0,0,0,0,
113,TIM+G+X,ML,gamma,3,3,1,DNA, -o lr -m 012230 -f m -a e -c 4,NA,,0,1,0,0,0,0,
114,GTR+G+X,ML,gamma,5,3,1,DNA, -o lr -m 012345 -f m -a e -c 4, -m GTRGAMMAX,,0,1,1,0,0,0,
115,LG+G,model,gamma,0,0,1,protein, -o lr -m LG -d aa -f m -a e -c 4, -m PROTGAMMALG,,1,1,0,0,1,0,
116,WAG+G,model,gamma,0,0,1,protein, -o lr -m WAG -d aa -f m -a e -c 4, -m PROTGAMMAWAG,,1,1,1,1,1,0,
117,MTREV+G,model,gamma,0,0,1,protein, -o lr -m mtREV -d aa -f m -a e -c 4, -m PROTGAMMAMTREV,,1,1,1,1,1,0,
118,DAYHOFF+G,model,gamma,0,0,1,protein, -o lr -m Dayhoff -d aa -f m -a e -c 4, -m PROTGAMMADAYHOFF,,1,1,1,1,1,0,
119,DCMUT+G,model,gamma,0,0,1,protein, -o lr -m DCMut -d aa -f m -a e -c 4, -m PROTGAMMADCMUT,,1,1,0,0,1,0,
120,JTT+G,model,gamma,0,0,1,protein, -o lr -m JTT -d aa -f m -a e -c 4, -m PROTGAMMAJTT,,1,1,1,0,1,0,
121,VT+G,model,gamma,0,0,1,protein, -o lr -m VT -d aa -f m -a e -c 4, -m PROTGAMMAVT,,1,1,0,1,1,0,
122,BLOSUM62+G,model,gamma,0,0,1,protein, -o lr -m Blosum62 -d aa -f m -a e -c 4, -m PROTGAMMABLOSUM62,,1,1,1,1,1,0,
123,CPREV+G,model,gamma,0,0,1,protein, -o lr -m CpREV -d aa -f m -a e -c 4, -m PROTGAMMACPREV,,1,1,1,1,1,0,
124,RTREV+G,model,gamma,0,0,1,protein, -o lr -m RtREV -d aa -f m -a e -c 4, -m PROTGAMMARTREV,,1,1,0,1,1,0,
125,MTMAM+G,model,gamma,0,0,1,protein, -o lr -m MtMam -d aa -f m -a e -c 4, -m PROTGAMMAMTMAM,,1,1,0,1,1,0,
126,MTART+G,model,gamma,0,0,1,protein, -o lr -m MtArt -d aa -f m -a e -c 4, -m PROTGAMMAMTART,,1,1,0,0,1,0,
127,HIVB+G,model,gamma,0,0,1,protein, -o lr -m HIVb -d aa -f m -a e -c 4, -m PROTGAMMAHIVB,,1,1,0,0,1,0,
128,HIVW+G,model,gamma,0,0,1,protein, -o lr -m HIVw -d aa -f m -a e -c 4, -m PROTGAMMAHIVW,,1,1,0,0,1,0,
129,LG4M+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMALG4M,,1,1,0,0,1,0,
130,LG4X+G,model,gamma,6,0,1,protein,NA,NA,"This model is not possible by definition, since the LG4X model has 4 free rate categories (i.e. they are not distributed according to a gamma distribution)",0,0,0,0,0,0,
131,MTZOA+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMAMTZOA,,1,1,0,0,1,0,
132,PMB+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMAPMB,,1,1,0,0,1,0,
133,JTTDCMUT+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMAJTTDCMUT,,1,1,0,0,1,0,
134,FLU+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMAFLU,,1,1,0,0,1,0,
135,STMTREV+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMASTMTREV,,1,1,0,0,1,0,
136,DUMMY+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMADUMMY,,1,1,0,0,1,0,
137,DUMMY2+G,model,gamma,0,0,1,protein,NA, -m PROTGAMMADUMMY2,,1,1,0,0,1,0,
138,GTR+G,model,gamma,189,0,1,protein,NA,NA,,0,1,0,0,0,0,
139,LG+G+F,empirical,gamma,0,19,1,protein, -o lr -m LG -d aa -f e -a e -c 4, -m PROTGAMMALGF,,1,1,0,0,1,0,
140,WAG+G+F,empirical,gamma,0,19,1,protein, -o lr -m WAG -d aa -f e -a e -c 4, -m PROTGAMMAWAGF,,1,1,0,1,1,0,
141,MTREV+G+F,empirical,gamma,0,19,1,protein, -o lr -m mtREV -d aa -f e -a e -c 4, -m PROTGAMMAMTREVF,,1,1,0,1,1,0,
142,DAYHOFF+G+F,empirical,gamma,0,19,1,protein, -o lr -m Dayhoff -d aa -f e -a e -c 4, -m PROTGAMMADAYHOFFF,,1,1,0,1,1,0,
143,DCMUT+G+F,empirical,gamma,0,19,1,protein, -o lr -m DCMut -d aa -f e -a e -c 4, -m PROTGAMMADCMUTF,,1,1,0,0,1,0,
144,JTT+G+F,empirical,gamma,0,19,1,protein, -o lr -m JTT -d aa -f e -a e -c 4, -m PROTGAMMAJTTF,,1,1,0,0,1,0,
145,VT+G+F,empirical,gamma,0,19,1,protein, -o lr -m VT -d aa -f e -a e -c 4, -m PROTGAMMAVTF,,1,1,0,1,1,0,
146,BLOSUM62+G+F,empirical,gamma,0,19,1,protein, -o lr -m Blosum62 -d aa -f e -a e -c 4, -m PROTGAMMABLOSUM62F,,1,1,0,1,1,0,
147,CPREV+G+F,empirical,gamma,0,19,1,protein, -o lr -m CpREV -d aa -f e -a e -c 4, -m PROTGAMMACPREVF,,1,1,0,1,1,0,
148,RTREV+G+F,empirical,gamma,0,19,1,protein, -o lr -m RtREV -d aa -f e -a e -c 4, -m PROTGAMMARTREVF,,1,1,0,1,1,0,
149,MTMAM+G+F,empirical,gamma,0,19,1,protein, -o lr -m MtMam -d aa -f e -a e -c 4, -m PROTGAMMAMTMAMF,,1,1,0,1,1,0,
150,MTART+G+F,empirical,gamma,0,19,1,protein, -o lr -m MtArt -d aa -f e -a e -c 4, -m PROTGAMMAMTARTF,,1,1,0,0,1,0,
151,HIVB+G+F,empirical,gamma,0,19,1,protein, -o lr -m HIVb -d aa -f e -a e -c 4, -m PROTGAMMAHIVBF,,1,1,0,0,1,0,
152,HIVW+G+F,empirical,gamma,0,19,1,protein, -o lr -m HIVw -d aa -f e -a e -c 4, -m PROTGAMMAHIVWF,,1,1,0,0,1,0,
153,LG4M+G+F,empirical,gamma,0,19,1,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
154,LG4X+G+F,empirical,gamma,6,19,1,protein,NA,NA,"This model is not possible by definition, since the LG4X model has 4 free rate categories (i.e. they are not distributed according to a gamma distribution)",0,0,0,0,0,0,
155,MTZOA+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMAMTZOAF,,1,1,0,0,1,0,
156,PMB+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMAPMBF,,1,1,0,0,1,0,
157,JTTDCMUT+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMAJTTDCMUTF,,1,1,0,0,1,0,
158,FLU+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMAFLUF,,1,1,0,0,1,0,
159,STMTREV+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMASTMTREVF,,1,1,0,0,1,0,
160,DUMMY+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMADUMMYF,,1,1,0,0,1,0,
161,DUMMY2+G+F,empirical,gamma,0,19,1,protein,NA, -m PROTGAMMADUMMY2F,,1,1,0,0,1,0,
162,GTR+G+F,empirical,gamma,189,19,1,protein,NA, -m PROTGAMMAGTR,,0,1,0,1,0,0,
163,LG+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMALGX,,0,1,0,0,0,0,
164,WAG+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAWAGX,,0,1,0,0,0,0,
165,MTREV+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAMTREVX,,0,1,0,0,0,0,
166,DAYHOFF+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMADAYHOFFX,,0,1,0,0,0,0,
167,DCMUT+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMADCMUTX,,0,1,0,0,0,0,
168,JTT+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAJTTX,,0,1,0,0,0,0,
169,VT+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAVTX,,0,1,0,0,0,0,
170,BLOSUM62+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMABLOSUM62X,,0,1,0,0,0,0,
171,CPREV+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMACPREVX,,0,1,0,0,0,0,
172,RTREV+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMARTREVX,,0,1,0,0,0,0,
173,MTMAM+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAMTMAMX,,0,1,0,0,0,0,
174,MTART+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAMTARTX,,0,1,0,0,0,0,
175,HIVB+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAHIVBX,,0,1,0,0,0,0,
176,HIVW+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAHIVWX,,0,1,0,0,0,0,
177,LG4M+G+X,ML,gamma,0,19,1,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
178,LG4X+G+X,ML,gamma,6,19,1,protein,NA,NA,"This model is not possible by definition, since the LG4X model has 4 free rate categories (i.e. they are not distributed according to a gamma distribution)",0,0,0,0,0,0,
179,MTZOA+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAMTZOAX,,0,1,0,0,0,0,
180,PMB+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAPMBX,,0,1,0,0,0,0,
181,JTTDCMUT+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAJTTDCMUTX,,0,1,0,0,0,0,
182,FLU+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMAFLUX,,0,1,0,0,0,0,
183,STMTREV+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMASTMTREVX,,0,1,0,0,0,0,
184,DUMMY+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMADUMMYX,,0,1,0,0,0,0,
185,DUMMY2+G+X,ML,gamma,0,19,1,protein,NA, -m PROTGAMMADUMMY2X,,0,1,0,0,0,0,
186,GTR+G+X,ML,gamma,189,19,1,protein,NA, -m PROTGAMMAGTRX,,0,1,0,0,0,0,
187,JC+I,equal,invariant,0,0,1,DNA," -o lr -m 000000 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,1,1,0,0,
188,K80+I,equal,invariant,1,0,1,DNA," -o lr -m 010010 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,1,1,0,0,
189,TRNEF+I,equal,invariant,2,0,1,DNA," -o lr -m 010020 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,1,0,0,0,
190,K81+I,equal,invariant,2,0,1,DNA," -o lr -m 012210 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,0,0,0,0,
191,TVMEF+I,equal,invariant,4,0,1,DNA," -o lr -m 012314 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,0,0,0,0,
192,TIMEF+I,equal,invariant,3,0,1,DNA," -o lr -m 012230 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,0,0,0,0,
193,SYM+I,equal,invariant,5,0,1,DNA," -o lr -m 012345 -f '0.25, 0.25, 0.25, 0.25' -v e -c 1",NA,,1,1,1,1,0,0,
194,F81+I,empirical,invariant,0,3,1,DNA, -o lr -m 000000 -f e -v e -c 1,NA,,1,1,0,1,0,0,
195,HKY+I,empirical,invariant,1,3,1,DNA, -o lr -m 010010 -f e -v e -c 1,NA,,1,1,1,1,0,0,
196,TRN+I,empirical,invariant,2,3,1,DNA, -o lr -m 010020 -f e -v e -c 1,NA,,1,1,1,0,0,0,
197,K81UF+I,empirical,invariant,2,3,1,DNA, -o lr -m 012210 -f e -v e -c 1,NA,,1,1,0,0,0,0,
198,TVM+I,empirical,invariant,4,3,1,DNA, -o lr -m 012314 -f e -v e -c 1,NA,,1,1,0,0,0,0,
199,TIM+I,empirical,invariant,3,3,1,DNA, -o lr -m 012230 -f e -v e -c 1,NA,,1,1,0,0,0,0,
200,GTR+I,empirical,invariant,5,3,1,DNA, -o lr -m 012345 -f e -v e -c 1,NA,,1,1,1,1,0,0,
201,F81+I+X,ML,invariant,0,3,1,DNA, -o lr -m 000000 -f m -v e -c 1,NA,,0,1,0,0,0,0,
202,HKY+I+X,ML,invariant,1,3,1,DNA, -o lr -m 010010 -f m -v e -c 1,NA,,0,1,1,0,0,0,
203,TRN+I+X,ML,invariant,2,3,1,DNA, -o lr -m 010020 -f m -v e -c 1,NA,,0,1,1,0,0,0,
204,K81UF+I+X,ML,invariant,2,3,1,DNA, -o lr -m 012210 -f m -v e -c 1,NA,,0,1,0,0,0,0,
205,TVM+I+X,ML,invariant,4,3,1,DNA, -o lr -m 012314 -f m -v e -c 1,NA,,0,1,0,0,0,0,
206,TIM+I+X,ML,invariant,3,3,1,DNA, -o lr -m 012230 -f m -v e -c 1,NA,,0,1,0,0,0,0,
207,GTR+I+X,ML,invariant,5,3,1,DNA, -o lr -m 012345 -f m -v e -c 1,NA,,0,1,1,0,0,0,
208,LG+I,model,invariant,0,0,1,protein, -o lr -m LG -d aa -f m -v e -c 1,NA,,1,1,0,0,0,0,
209,WAG+I,model,invariant,0,0,1,protein, -o lr -m WAG -d aa -f m -v e -c 1,NA,,1,1,1,1,0,0,
210,MTREV+I,model,invariant,0,0,1,protein, -o lr -m mtREV -d aa -f m -v e -c 1,NA,,1,1,1,1,0,0,
211,DAYHOFF+I,model,invariant,0,0,1,protein, -o lr -m Dayhoff -d aa -f m -v e -c 1,NA,,1,1,1,1,0,0,
212,DCMUT+I,model,invariant,0,0,1,protein, -o lr -m DCMut -d aa -f m -v e -c 1,NA,,1,1,0,0,0,0,
213,JTT+I,model,invariant,0,0,1,protein, -o lr -m JTT -d aa -f m -v e -c 1,NA,,1,1,1,0,0,0,
214,VT+I,model,invariant,0,0,1,protein, -o lr -m VT -d aa -f m -v e -c 1,NA,,1,1,0,1,0,0,
215,BLOSUM62+I,model,invariant,0,0,1,protein, -o lr -m Blosum62 -d aa -f m -v e -c 1,NA,,1,1,1,1,0,0,
216,CPREV+I,model,invariant,0,0,1,protein, -o lr -m CpREV -d aa -f m -v e -c 1,NA,,1,1,1,1,0,0,
217,RTREV+I,model,invariant,0,0,1,protein, -o lr -m RtREV -d aa -f m -v e -c 1,NA,,1,1,0,1,0,0,
218,MTMAM+I,model,invariant,0,0,1,protein, -o lr -m MtMam -d aa -f m -v e -c 1,NA,,1,1,0,1,0,0,
219,MTART+I,model,invariant,0,0,1,protein, -o lr -m MtArt -d aa -f m -v e -c 1,NA,,1,1,0,0,0,0,
220,HIVB+I,model,invariant,0,0,1,protein, -o lr -m HIVb -d aa -f m -v e -c 1,NA,,1,1,0,0,0,0,
221,HIVW+I,model,invariant,0,0,1,protein, -o lr -m HIVw -d aa -f m -v e -c 1,NA,,1,1,0,0,0,0,
222,LG4M+I,model,invariant,0,0,1,protein,NA,NA,,0,1,0,0,0,0,
223,LG4X+I,model,invariant,6,0,1,protein,NA,NA,,0,1,0,0,0,0,
224,MTZOA+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
225,PMB+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
226,JTTDCMUT+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
227,FLU+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
228,STMTREV+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
229,DUMMY+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
230,DUMMY2+I,model,invariant,0,0,1,protein,NA,NA,,1,1,0,0,0,0,
231,GTR+I,model,invariant,189,0,1,protein,NA,NA,"Not possilbe by definition, since the GTR model has to get it's amino acid frequencies from somewhere.",0,1,0,0,0,0,
232,LG+I+F,empirical,invariant,0,19,1,protein, -o lr -m LG -d aa -f e -v e -c 1,NA,,1,1,0,0,0,0,
233,WAG+I+F,empirical,invariant,0,19,1,protein, -o lr -m WAG -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
234,MTREV+I+F,empirical,invariant,0,19,1,protein, -o lr -m mtREV -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
235,DAYHOFF+I+F,empirical,invariant,0,19,1,protein, -o lr -m Dayhoff -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
236,DCMUT+I+F,empirical,invariant,0,19,1,protein, -o lr -m DCMut -d aa -f e -v e -c 1,NA,,1,1,0,0,0,0,
237,JTT+I+F,empirical,invariant,0,19,1,protein, -o lr -m JTT -d aa -f e -v e -c 1,NA,,1,1,0,0,0,0,
238,VT+I+F,empirical,invariant,0,19,1,protein, -o lr -m VT -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
239,BLOSUM62+I+F,empirical,invariant,0,19,1,protein, -o lr -m Blosum62 -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
240,CPREV+I+F,empirical,invariant,0,19,1,protein, -o lr -m CpREV -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
241,RTREV+I+F,empirical,invariant,0,19,1,protein, -o lr -m RtREV -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
242,MTMAM+I+F,empirical,invariant,0,19,1,protein, -o lr -m MtMam -d aa -f e -v e -c 1,NA,,1,1,0,1,0,0,
243,MTART+I+F,empirical,invariant,0,19,1,protein, -o lr -m MtArt -d aa -f e -v e -c 1,NA,,1,1,0,0,0,0,
244,HIVB+I+F,empirical,invariant,0,19,1,protein, -o lr -m HIVb -d aa -f e -v e -c 1,NA,,1,1,0,0,0,0,
245,HIVW+I+F,empirical,invariant,0,19,1,protein, -o lr -m HIVw -d aa -f e -v e -c 1,NA,,1,1,0,0,0,0,
246,LG4M+I+F,empirical,invariant,0,19,1,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
247,LG4X+I+F,empirical,invariant,6,19,1,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
248,MTZOA+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
249,PMB+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
250,JTTDCMUT+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
251,FLU+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
252,STMTREV+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
253,DUMMY+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
254,DUMMY2+I+F,empirical,invariant,0,19,1,protein,NA,NA,,1,1,0,0,0,0,
255,GTR+I+F,empirical,invariant,189,19,1,protein,NA,NA,,0,1,0,1,0,0,
256,LG+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
257,WAG+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
258,MTREV+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
259,DAYHOFF+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
260,DCMUT+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
261,JTT+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
262,VT+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
263,BLOSUM62+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
264,CPREV+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
265,RTREV+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
266,MTMAM+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
267,MTART+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
268,HIVB+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
269,HIVW+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
270,LG4M+I+X,ML,invariant,0,19,1,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
271,LG4X+I+X,ML,invariant,6,19,1,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
272,MTZOA+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
273,PMB+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
274,JTTDCMUT+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
275,FLU+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
276,STMTREV+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
277,DUMMY+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
278,DUMMY2+I+X,ML,invariant,0,19,1,protein,NA,NA,,0,1,0,0,0,0,
279,GTR+I+X,ML,invariant,189,19,1,protein,NA,NA,,0,1,0,0,0,0,
280,JC+I+G,equal,"invariant, gamma",0,0,2,DNA," -o lr -m 000000 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,1,1,0,1,
281,K80+I+G,equal,"invariant, gamma",1,0,2,DNA," -o lr -m 010010 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,1,1,0,1,
282,TRNEF+I+G,equal,"invariant, gamma",2,0,2,DNA," -o lr -m 010020 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,1,0,0,1,
283,K81+I+G,equal,"invariant, gamma",2,0,2,DNA," -o lr -m 012210 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,0,0,0,1,
284,TVMEF+I+G,equal,"invariant, gamma",4,0,2,DNA," -o lr -m 012314 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,0,0,0,1,
285,TIMEF+I+G,equal,"invariant, gamma",3,0,2,DNA," -o lr -m 012230 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,0,0,0,1,
286,SYM+I+G,equal,"invariant, gamma",5,0,2,DNA," -o lr -m 012345 -f '0.25, 0.25, 0.25, 0.25' -v e -a e -c 4",NA,,1,1,1,1,0,1,
287,F81+I+G,empirical,"invariant, gamma",0,3,2,DNA, -o lr -m 000000 -f e -v e -a e -c 4,NA,,1,1,0,1,0,1,
288,HKY+I+G,empirical,"invariant, gamma",1,3,2,DNA, -o lr -m 010010 -f e -v e -a e -c 4,NA,,1,1,1,1,0,1,
289,TRN+I+G,empirical,"invariant, gamma",2,3,2,DNA, -o lr -m 010020 -f e -v e -a e -c 4,NA,,1,1,1,0,0,1,
290,K81UF+I+G,empirical,"invariant, gamma",2,3,2,DNA, -o lr -m 012210 -f e -v e -a e -c 4,NA,,1,1,0,0,0,1,
291,TVM+I+G,empirical,"invariant, gamma",4,3,2,DNA, -o lr -m 012314 -f e -v e -a e -c 4,NA,,1,1,0,0,0,1,
292,TIM+I+G,empirical,"invariant, gamma",3,3,2,DNA, -o lr -m 012230 -f e -v e -a e -c 4,NA,,1,1,0,0,0,1,
293,GTR+I+G,empirical,"invariant, gamma",5,3,2,DNA, -o lr -m 012345 -f e -v e -a e -c 4, -m GTRGAMMAI,,1,1,1,1,0,1,
294,F81+I+G+X,ML,"invariant, gamma",0,3,2,DNA, -o lr -m 000000 -f m -v e -a e -c 4,NA,,0,1,0,0,0,0,
295,HKY+I+G+X,ML,"invariant, gamma",1,3,2,DNA, -o lr -m 010010 -f m -v e -a e -c 4,NA,,0,1,1,0,0,0,
296,TRN+I+G+X,ML,"invariant, gamma",2,3,2,DNA, -o lr -m 010020 -f m -v e -a e -c 4,NA,,0,1,1,0,0,0,
297,K81UF+I+G+X,ML,"invariant, gamma",2,3,2,DNA, -o lr -m 012210 -f m -v e -a e -c 4,NA,,0,1,0,0,0,0,
298,TVM+I+G+X,ML,"invariant, gamma",4,3,2,DNA, -o lr -m 012314 -f m -v e -a e -c 4,NA,,0,1,0,0,0,0,
299,TIM+I+G+X,ML,"invariant, gamma",3,3,2,DNA, -o lr -m 012230 -f m -v e -a e -c 4,NA,,0,1,0,0,0,0,
300,GTR+I+G+X,ML,"invariant, gamma",5,3,2,DNA, -o lr -m 012345 -f m -v e -a e -c 4, -m GTRGAMMAIX,,0,1,1,0,0,0,
301,LG+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m LG -d aa -f m -v e -a e -c 4, -m PROTGAMMAILG,,1,1,0,0,0,1,
302,WAG+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m WAG -d aa -f m -v e -a e -c 4, -m PROTGAMMAIWAG,,1,1,1,1,0,1,
303,MTREV+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m mtREV -d aa -f m -v e -a e -c 4, -m PROTGAMMAIMTREV,,1,1,1,1,0,1,
304,DAYHOFF+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m Dayhoff -d aa -f m -v e -a e -c 4, -m PROTGAMMAIDAYHOFF,,1,1,1,1,0,1,
305,DCMUT+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m DCMut -d aa -f m -v e -a e -c 4, -m PROTGAMMAIDCMUT,,1,1,0,0,0,1,
306,JTT+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m JTT -d aa -f m -v e -a e -c 4, -m PROTGAMMAIJTT,,1,1,1,0,0,1,
307,VT+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m VT -d aa -f m -v e -a e -c 4, -m PROTGAMMAIVT,,1,1,0,1,0,1,
308,BLOSUM62+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m Blosum62 -d aa -f m -v e -a e -c 4, -m PROTGAMMAIBLOSUM62,,1,1,1,1,0,1,
309,CPREV+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m CpREV -d aa -f m -v e -a e -c 4, -m PROTGAMMAICPREV,,1,1,1,1,0,1,
310,RTREV+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m RtREV -d aa -f m -v e -a e -c 4, -m PROTGAMMAIRTREV,,1,1,0,1,0,1,
311,MTMAM+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m MtMam -d aa -f m -v e -a e -c 4, -m PROTGAMMAIMTMAM,,1,1,0,1,0,1,
312,MTART+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m MtArt -d aa -f m -v e -a e -c 4, -m PROTGAMMAIMTART,,1,1,0,0,0,1,
313,HIVB+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m HIVb -d aa -f m -v e -a e -c 4, -m PROTGAMMAIHIVB,,1,1,0,0,0,1,
314,HIVW+I+G,model,"invariant, gamma",0,0,2,protein, -o lr -m HIVw -d aa -f m -v e -a e -c 4, -m PROTGAMMAIHIVW,,1,1,0,0,0,1,
315,LG4M+I+G,model,"invariant, gamma",0,0,2,protein,NA,NA,Not implemented in RAxML,0,0,0,0,0,0,
316,LG4X+I+G,model,"invariant, gamma",6,0,2,protein,NA,NA,"This model is not possible by definition, since the LG4X model has 4 free rate categories (i.e. they are not distributed according to a gamma distribution)",0,1,0,0,0,0,
317,MTZOA+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAIMTZOA,,1,1,0,0,0,1,
318,PMB+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAIPMB,,1,1,0,0,0,1,
319,JTTDCMUT+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAIJTTDCMUT,,1,1,0,0,0,1,
320,FLU+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAIFLU,,1,1,0,0,0,1,
321,STMTREV+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAISTMTREV,,1,1,0,0,0,1,
322,DUMMY+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAIDUMMY,,1,1,0,0,0,1,
323,DUMMY2+I+G,model,"invariant, gamma",0,0,2,protein,NA, -m PROTGAMMAIDUMMY2,,1,1,0,0,0,1,
324,GTR+I+G,model,"invariant, gamma",189,0,2,protein,NA,NA,"Not possilbe by definition, since the GTR model has to get it's amino acid frequencies from somewhere.",0,0,0,0,0,0,
325,LG+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m LG -d aa -f e -v e -a e -c 4, -m PROTGAMMAILGF,,1,1,0,0,0,1,
326,WAG+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m WAG -d aa -f e -v e -a e -c 4, -m PROTGAMMAIWAGF,,1,1,0,1,0,1,
327,MTREV+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m mtREV -d aa -f e -v e -a e -c 4, -m PROTGAMMAIMTREVF,,1,1,0,1,0,1,
328,DAYHOFF+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m Dayhoff -d aa -f e -v e -a e -c 4, -m PROTGAMMAIDAYHOFFF,,1,1,0,1,0,1,
329,DCMUT+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m DCMut -d aa -f e -v e -a e -c 4, -m PROTGAMMAIDCMUTF,,1,1,0,0,0,1,
330,JTT+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m JTT -d aa -f e -v e -a e -c 4, -m PROTGAMMAIJTTF,,1,1,0,0,0,1,
331,VT+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m VT -d aa -f e -v e -a e -c 4, -m PROTGAMMAIVTF,,1,1,0,1,0,1,
332,BLOSUM62+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m Blosum62 -d aa -f e -v e -a e -c 4, -m PROTGAMMAIBLOSUM62F,,1,1,0,1,0,1,
333,CPREV+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m CpREV -d aa -f e -v e -a e -c 4, -m PROTGAMMAICPREVF,,1,1,0,1,0,1,
334,RTREV+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m RtREV -d aa -f e -v e -a e -c 4, -m PROTGAMMAIRTREVF,,1,1,0,1,0,1,
335,MTMAM+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m MtMam -d aa -f e -v e -a e -c 4, -m PROTGAMMAIMTMAMF,,1,1,0,1,0,1,
336,MTART+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m MtArt -d aa -f e -v e -a e -c 4, -m PROTGAMMAIMTARTF,,1,1,0,0,0,1,
337,HIVB+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m HIVb -d aa -f e -v e -a e -c 4, -m PROTGAMMAIHIVBF,,1,1,0,0,0,1,
338,HIVW+I+G+F,empirical,"invariant, gamma",0,19,2,protein, -o lr -m HIVw -d aa -f e -v e -a e -c 4, -m PROTGAMMAIHIVWF,,1,1,0,0,0,1,
339,LG4M+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
340,LG4X+I+G+F,empirical,"invariant, gamma",6,19,2,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
341,MTZOA+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIMTZOAF,,1,1,0,0,0,1,
342,PMB+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIPMBF,,1,1,0,0,0,1,
343,JTTDCMUT+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIJTTDCMUTF,,1,1,0,0,0,1,
344,FLU+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIFLUF,,1,1,0,0,0,1,
345,STMTREV+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAISTMTREVF,,1,1,0,0,0,1,
346,DUMMY+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIDUMMYF,,1,1,0,0,0,1,
347,DUMMY2+I+G+F,empirical,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIDUMMY2F,,1,1,0,0,0,1,
348,GTR+I+G+F,empirical,"invariant, gamma",189,19,2,protein,NA, -m PROTGAMMAIGTR,,0,1,0,1,0,0,
349,LG+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAILGX,,0,1,0,0,0,0,
350,WAG+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIWAGX,,0,1,0,0,0,0,
351,MTREV+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIMTREVX,,0,1,0,0,0,0,
352,DAYHOFF+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIDAYHOFFX,,0,1,0,0,0,0,
353,DCMUT+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIDCMUTX,,0,1,0,0,0,0,
354,JTT+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIJTTX,,0,1,0,0,0,0,
355,VT+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIVTX,,0,1,0,0,0,0,
356,BLOSUM62+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIBLOSUM62X,,0,1,0,0,0,0,
357,CPREV+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAICPREVX,,0,1,0,0,0,0,
358,RTREV+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIRTREVX,,0,1,0,0,0,0,
359,MTMAM+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIMTMAMX,,0,1,0,0,0,0,
360,MTART+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIMTARTX,,0,1,0,0,0,0,
361,HIVB+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIHIVBX,,0,1,0,0,0,0,
362,HIVW+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIHIVWX,,0,1,0,0,0,0,
363,LG4M+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
364,LG4X+I+G+X,ML,"invariant, gamma",6,19,2,protein,NA,NA,"Advised against in the RAxML v8 Manual, so not impelemented in PF",0,0,0,0,0,0,
365,MTZOA+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIMTZOAX,,0,1,0,0,0,0,
366,PMB+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIPMBX,,0,1,0,0,0,0,
367,JTTDCMUT+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIJTTDCMUTX,,0,1,0,0,0,0,
368,FLU+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIFLUX,,0,1,0,0,0,0,
369,STMTREV+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAISTMTREVX,,0,1,0,0,0,0,
370,DUMMY+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIDUMMYX,,0,1,0,0,0,0,
371,DUMMY2+I+G+X,ML,"invariant, gamma",0,19,2,protein,NA, -m PROTGAMMAIDUMMY2X,,0,1,0,0,0,0,
372,GTR+I+G+X,ML,"invariant, gamma",189,19,2,protein,NA, -m PROTGAMMAIGTRX,,0,1,0,0,0,0,
\ No newline at end of file
diff --git a/partfinder/neighbour.py b/partfinder/neighbour.py
new file mode 100644
index 0000000..20228d1
--- /dev/null
+++ b/partfinder/neighbour.py
@@ -0,0 +1,287 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import subset_ops
+import scheme
+import numpy as np
+import scipy.spatial.distance
+import itertools
+from util import PartitionFinderError
+
+import logtools
+log = logtools.get_logger()
+
+
+def get_ranked_list(distance_matrix, subsets, N):
+ """
+ Return the N closest pairs of subsets in 'subsets'
+ """
+
+ # TODO. If/when anaconda moves to numpy v1.8, we can use
+ # a ~7x faster solution here, which uses np.argpartition()
+ # see here: http://stackoverflow.com/questions/20540889/
+ # extract-the-n-closest-pairs-from-a-numpy-distance-array
+ closest = distance_matrix.argsort()[:N]
+ n = len(subsets)
+ ti = np.triu_indices(n, 1)
+ r = zip(ti[0][closest] + 1, ti[1][closest] + 1)
+
+ # and we look up all the subsets that correspond to each distance
+ # and add it to our ordered list of subset lists
+ ordered_subsets = []
+ for i, pair in enumerate(r):
+ subset_group = [subsets[i-1] for i in pair]
+ ordered_subsets.append(subset_group)
+
+ return ordered_subsets
+
+def get_manhattan_matrix(rates, freqs, model, alpha, weights):
+
+ # get distances between all pairs for all nonzero weights
+ # for each matrix we then normalise and weight it
+ # by multiplying by the weight/max
+ distance_arrays = []
+
+ if weights["rate"] > 0:
+ r_dists = scipy.spatial.distance.pdist(np.array(rates), 'cityblock')
+ if np.amax(r_dists)>0:
+ norm = float(weights["rate"])/float(np.amax(r_dists))
+ r_dists = np.multiply(r_dists, norm)
+ distance_arrays.append(r_dists)
+ if weights["freqs"] > 0:
+ f_dists = scipy.spatial.distance.pdist(np.array(freqs), 'cityblock')
+ if np.amax(f_dists)>0:
+ norm = float(weights["freqs"])/float(np.amax(f_dists))
+ f_dists = np.multiply(f_dists, norm)
+ distance_arrays.append(f_dists)
+ if weights["model"] > 0:
+ m_dists = scipy.spatial.distance.pdist(np.array(model), 'cityblock')
+ if np.amax(m_dists)>0:
+ norm = float(weights["model"])/float(np.amax(m_dists))
+ m_dists = np.multiply(m_dists, norm)
+ distance_arrays.append(m_dists)
+ if weights["alpha"] > 0:
+ a_dists = scipy.spatial.distance.pdist(np.array(alpha), 'cityblock')
+ if np.amax(a_dists)>0:
+ norm = float(weights["alpha"])/float(np.amax(a_dists))
+ a_dists = np.multiply(a_dists, norm)
+ distance_arrays.append(a_dists)
+
+ try:
+ final_dists = distance_arrays[0]
+ except:
+ # no distance arrays, something odd happened
+ log.error("Problem calculating subset similarity. Please check that you included"
+ " at least one non-zero weight in your clustering weights")
+ raise PartitionFinderError
+
+ for a in distance_arrays[1:]:
+ try:
+ final_dists = np.add(final_dists, a)
+ except:
+ log.error("Distance matrices from different parameters are not the same size")
+ raise PartitionFinderError
+
+ return final_dists
+
+def get_distance_matrix(subsets, weights):
+
+ #1. get the parameter lists for each subset
+ rates = [] # tree length
+ freqs = [] # amino acid or base frequencies
+ model = [] # model parameters e.g. A<->C
+ alpha = [] #alpha parameter of the gamma distribution of rates across sites
+
+ for s in subsets:
+ param_dict = s.get_param_values()
+ rates.append([param_dict["rate"]])
+ freqs.append(param_dict["freqs"])
+ model.append(param_dict["model"])
+ alpha.append([param_dict["alpha"]])
+
+ # get pairwise manhattan distances between subsets (a square numpy array)
+ final_dists = get_manhattan_matrix(rates, freqs, model, alpha, weights)
+
+ return final_dists
+
+def get_N_closest_subsets(subsets, cfg, N, distance_matrix = np.matrix([])):
+ """Find the N most similar groups of subsets in a scheme
+ """
+
+ if not distance_matrix.any():
+ distance_matrix = get_distance_matrix(subsets, cfg.cluster_weights)
+ ranked_subset_groupings = get_ranked_list(distance_matrix, subsets, N)
+ return ranked_subset_groupings
+
+
+def make_clustered_scheme(start_scheme, scheme_name, subsets_to_cluster, merged_sub, cfg):
+
+ # 1. Then we define a new scheme with those merged subsets
+ new_subsets = start_scheme.subsets - set(subsets_to_cluster)
+ new_subsets.add(merged_sub)
+
+ #3. Create the clustered scheme
+ final_scheme = scheme.Scheme(cfg, str(scheme_name), new_subsets)
+
+ return final_scheme
+
+
+def make_split_scheme(start_scheme, scheme_name, subset_to_split, split_subsets, cfg):
+
+ # 1. Then we define a new scheme with those merged subsets
+ new_subsets = start_scheme.subsets - {subset_to_split}
+
+ # 2. add all of the split subsets
+ for s in split_subsets:
+ new_subsets.add(s)
+
+ #3. Create the clustered scheme
+ final_scheme = scheme.Scheme(cfg, str(scheme_name), new_subsets)
+
+ return final_scheme
+
+
+def get_nearest_neighbour_scheme(start_scheme, scheme_name, cfg):
+ """
+ The idea here is to take a scheme, and perform some analyses to find a
+ neighbouring scheme, where the neighbour has one less subset than the
+ current scheme. Really this is just progressive clustering, but specified
+ to work well with PartitionFinder
+ """
+
+ # we use [0] becuase the function returns a ranked list of lists of length 1
+ subsets = [s for s in start_scheme.subsets]
+ closest_subsets = get_N_closest_subsets(subsets, cfg, 1)[0]
+
+ merged_sub = subset_ops.merge_subsets(closest_subsets)
+
+ scheme = make_clustered_scheme(
+ start_scheme, scheme_name, closest_subsets, merged_sub, cfg)
+
+ return scheme
+
+
+
+
+def update_c_matrix(c_matrix, sub_tuples, subsets, diffs):
+ """
+ Update a symmetric matrix of measurements between subsets.
+ Each subset_tuple contains a new subset that is just merged
+ from a collection of old subsets.
+ """
+ if len(c_matrix.shape) == 1:
+ c_matrix = scipy.spatial.distance.squareform(c_matrix)
+
+ for t, diff in itertools.izip(sub_tuples, diffs):
+ old_subs = t[1]
+ i = subsets.index(old_subs[0])
+ j = subsets.index(old_subs[1])
+ c_matrix[i,j] = c_matrix[j,i] = diff
+
+ return c_matrix
+
+def get_best_pair(c_matrix, best_change, subsets):
+
+ log.debug("C matrix: %s", str(c_matrix))
+
+ if len(c_matrix.shape) == 1:
+ log.debug("C matrix shape was == 1")
+ c_matrix = scipy.spatial.distance.squareform(c_matrix)
+ log.debug("C matrix: %s", str(c_matrix))
+
+ l = np.where(c_matrix==best_change)
+
+ log.debug("C matrix dimensions: %s", str(c_matrix.shape))
+ log.debug("Number of subsets: %d", len(subsets))
+ log.debug("Location of best_change in c_matrix: %s", str(l))
+
+ # this function is only called if the best_change is <0
+ # so we can be sure that we are on an off-diagonal
+ # still, we check and throw an error if there's an issue
+ s1 = l[0][0]
+ s2 = l[1][0]
+
+ if s1==s2:
+ log.error("You can't merge a subset with itself, please check.")
+ raise PartitionFinderError
+
+ log.debug("Subsets to merge: %s and %s" %(s1, s2))
+ sub1 = subsets[s1]
+ sub2 = subsets[s2]
+ return (sub1, sub2)
+
+def reset_c_matrix(c_matrix, remove_list, add_list, subsets):
+
+ if len(c_matrix.shape) == 1:
+ c_matrix = scipy.spatial.distance.squareform(c_matrix)
+
+ indices = []
+ removals = []
+ for r in remove_list:
+ indices.append(subsets.index(r))
+ removals = removals + r.names
+
+ c_matrix = np.delete(c_matrix, indices, 1)
+ c_matrix = np.delete(c_matrix, indices, 0)
+
+ additions = []
+ for a in add_list:
+ additions = additions + a.names
+ row = np.array((c_matrix.shape[0]) * [np.inf])
+ col = c_matrix.shape[0] * [np.inf]
+ col.append(0)
+ col = np.array(col)[:, None]
+ c_matrix = np.vstack((c_matrix, row))
+ c_matrix = np.hstack((c_matrix, col))
+
+ # we can only do this if we've removed the same stuff as we added, check
+ if not additions.sort() == removals.sort():
+ log.error("Removal and addition of subsets don't add up")
+ log.error("Removing: %s", str(removals))
+ log.error("Adding: %s", str(additions))
+ raise PartitionFinderError
+
+ return c_matrix
+
+def reset_subsets(subsets, remove_list, add_list):
+
+ log.debug("Updating subset list")
+ log.debug("Original subset list: %s", str([s.name for s in subsets]))
+ log.debug("Subsets to remove: %s", str([s.name for s in remove_list]))
+ log.debug("Combined subsets to add: %s", str([s.name for s in add_list]))
+
+ for r in remove_list:
+ subsets.pop(subsets.index(r))
+ for a in add_list:
+ subsets.append(a)
+ return subsets
+
+
+def get_pairs_todo(closest_pairs, c_matrix, subsets):
+ pairs_todo = []
+ if len(c_matrix.shape) == 1:
+ c_matrix = scipy.spatial.distance.squareform(c_matrix)
+
+ for p in closest_pairs:
+ i = subsets.index(p[0])
+ j = subsets.index(p[1])
+ if c_matrix[i,j] == np.inf:
+ pairs_todo.append(p)
+
+ return pairs_todo
+
+
diff --git a/partfinder/parser.py b/partfinder/parser.py
new file mode 100644
index 0000000..57d82f6
--- /dev/null
+++ b/partfinder/parser.py
@@ -0,0 +1,310 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+from pyparsing import (
+ Word, OneOrMore, alphas, nums, Suppress, Optional, Group, stringEnd,
+ delimitedList, pythonStyleComment, line, lineno, col, Keyword,
+ ParseException )
+
+# Use this for debugging
+# ParserElement.verbose_stacktrace = True
+
+import scheme
+import subset
+import subset_ops
+import config
+import model_loader as mo
+from util import PartitionFinderError
+
+
+class ParserError(Exception):
+ """Used for our own parsing problems"""
+ def __init__(self, text, loc, msg):
+ self.line = line(loc, text)
+ self.col = col(loc, text)
+ self.lineno = lineno(loc, text)
+ self.msg = msg
+
+ def format_message(self):
+ return "%s at line:%s, column:%s" % (self.msg, self.lineno, self.col)
+
+
+class Parser(object):
+ """Parse configuration files
+
+ The results are put into the configuration object
+ """
+ def __init__(self, cfg):
+ """Construct parser from the configuration
+ """
+ self.cfg = cfg
+
+ # Use these to keep track of stuff that is going on in parser
+ self.schemes = []
+ self.current_subsets = []
+ self.init_grammar()
+ self.ignore_schemes = False
+
+ def init_grammar(self):
+ """Set up the parsing classes
+ Any changes to the grammar of the config file be done here.
+ """
+
+ # Some syntax that we need, but don't care about
+ SEMICOLON = (Suppress(";"))
+ EQUALS = Suppress("=")
+
+ # Top Section
+ FILE_NAME = Word(alphas + nums + '-_.')
+ alignment_def = Keyword('alignment') + EQUALS\
+ + FILE_NAME + SEMICOLON
+ alignment_def.setParseAction(self.set_alignment)
+
+ tree_def = Keyword('user_tree_topology') + EQUALS\
+ + FILE_NAME + SEMICOLON
+ tree_def.setParseAction(self.set_user_tree)
+
+ def simple_option(name):
+ opt = Keyword(name) + EQUALS +\
+ Word(alphas + nums + '-_') + SEMICOLON
+ opt.setParseAction(self.set_simple_option)
+ return opt
+
+ branch_def = simple_option('branchlengths')
+
+ MODEL_NAME = Word(alphas + nums + '+' + ' ' + '_')
+ model_list = delimitedList(MODEL_NAME)
+ model_def = 'models' + EQUALS + model_list + SEMICOLON
+ model_def.setParseAction(self.set_models)
+
+ model_selection_def = simple_option("model_selection")
+ top_section = alignment_def + Optional(tree_def) + branch_def + \
+ model_def + model_selection_def
+
+
+ # Data Block Parsing
+ column = Word(nums)
+ block_name = Word(alphas + '_-' + nums)
+ block_def = column("start") +\
+ Optional(Suppress("-") + column("end")) +\
+ Optional(Suppress("\\") + column("step"))
+ block_def.setParseAction(self.define_range)
+
+ block_list_def = Group(OneOrMore(Group(block_def)))
+
+ user_subset_def = Optional("charset") + block_name("name") + \
+ EQUALS + block_list_def("parts") + SEMICOLON
+ user_subset_def.setParseAction(self.define_user_subset)
+
+ block_def_list = OneOrMore(Group(user_subset_def))
+ block_section = Suppress("[data_blocks]") + block_def_list
+ block_def_list.setParseAction(self.check_blocks)
+
+ # Scheme Parsing
+ scheme_name = Word(alphas + '_-' + nums)
+
+ # Make a copy, cos we set a different action on it
+ user_subset_ref = block_name.copy()
+ user_subset_ref.setParseAction(self.check_block_exists)
+
+ subset = Group(Suppress("(") +
+ delimitedList(user_subset_ref("name")) + Suppress(")"))
+ subset.setParseAction(self.define_subset_grouping)
+
+ scheme = Group(OneOrMore(subset))
+ scheme_def = scheme_name("name") + \
+ EQUALS + scheme("scheme") + SEMICOLON
+ scheme_def.setParseAction(self.define_scheme)
+
+ scheme_list = OneOrMore(Group(scheme_def))
+
+ scheme_algo = simple_option("search")
+ scheme_section = \
+ Suppress("[schemes]") + scheme_algo + Optional(scheme_list)
+
+ # We've defined the grammar for each section.
+ # Here we just put it all together
+ self.config_parser = (
+ top_section + block_section + scheme_section + stringEnd)
+
+ def set_alignment(self, text, loc, tokens):
+ value = tokens[1]
+ self.cfg.set_alignment_file(value)
+
+ def set_user_tree(self, tokens):
+ self.cfg.user_tree = tokens[1]
+
+ def set_simple_option(self, text, loc, tokens):
+ try:
+ self.cfg.set_option(tokens[0], tokens[1])
+ except config.ConfigurationError:
+ raise ParserError(text, loc, "Invalid option in .cfg file")
+
+ def define_range(self, text, loc, part):
+ """Turn the 1, 2 or 3 tokens into integers: from:to/step
+ """
+ from_column = int(part.start)
+
+ if part.end:
+ to_column = int(part.end)
+ else:
+ to_column = from_column
+
+ if part.step:
+ step = int(part.step)
+ else:
+ step = 1
+
+ if from_column > to_column:
+ raise ParserError(
+ text, loc, "Data block has must have beginning less than end "
+ "(%d is great than %d)" % (from_column, to_column))
+ return [from_column, to_column, step]
+
+ def define_user_subset(self, text, loc, part_def):
+ """Use a list of tuples with start,stop,step to produces columns"""
+
+ # We need to convert to column definitions. Note that these are
+ # zero based, which is not how they are specified in the config. So we
+ # must do some fiddling to make sure they are right. In addition, we
+ # use range(...) which excludes the final column, whereas the
+ # definitions assume inclusive. Subtracting 1 from start deals with
+ # both issues...
+ columns = []
+ description = []
+ for start, stop, step in part_def.parts:
+ columns.extend(range(start-1, stop, step))
+
+ # Keep a description of this around
+ description.append((start, stop, step))
+
+ # Normalise it all
+ column_set = set(columns)
+
+ # If there was any overlap then these will differ...
+ if len(columns) != len(column_set):
+ raise ParserError(
+ text, loc, "Block '%s' has internal overlap" % part_def.name)
+
+ user_subset = subset.Subset(self.cfg, column_set)
+ user_subset.add_description([part_def.name], description)
+
+ self.cfg.user_subsets.append(user_subset)
+ self.cfg.user_subsets_by_name[part_def.name] = user_subset
+
+ def check_blocks(self, text, loc, partref):
+ # Make sure that the user subsets don't overlap.
+ ov = subset_ops.subsets_overlap(self.cfg.user_subsets)
+ if ov:
+ raise ParserError(text, loc, "The following sites overlap "
+ " in your block definitions: %s. "
+ "Please change the configuration so each "
+ "site occurs in only one block" % ", ".join(map(str, ov)))
+
+ def check_block_exists(self, text, loc, partref):
+ if partref.name not in self.cfg.user_subsets_by_name:
+ raise ParserError(text, loc, "Block %s not defined" %
+ partref.name)
+
+ def define_subset_grouping(self, text, loc, subset_def):
+ """These define initial groupings that users think are useful
+ """
+ try:
+ # Get the partitions from the names
+ subsets = [self.cfg.user_subsets_by_name[nm] for nm in subset_def[0]]
+
+ # Keep a running list of these till we define the schema below
+ self.current_subsets.append(subset_ops.merge_subsets(subsets))
+ except subset.SubsetError:
+ raise ParserError(text, loc, "Error creating subset...")
+
+ def define_scheme(self, text, loc, scheme_def):
+ try:
+ subs = tuple(self.current_subsets)
+
+ if not self.ignore_schemes:
+ sch = scheme.Scheme(self.cfg, scheme_def.name, subs)
+ self.cfg.user_schemes.add_scheme(sch)
+
+ except (scheme.SchemeError, subset.SubsetError):
+ raise ParserError(text, loc, "Error in '%s' can be found" %
+ scheme_def.name)
+ finally:
+ # Clear out the current_subsets as we need to reuse it
+ self.current_subsets = []
+
+
+ def parse_file(self, file_name):
+ #this just reads in the config file into 's'
+ s = open(file_name, 'rU').read()
+ self.parse_configuration(s)
+
+ def parse_configuration(self, s):
+ """Parse a string as a configuration settings file"""
+ try:
+ self.result = self.config_parser.ignore(pythonStyleComment).\
+ parseString(s)
+
+ except ParserError, p:
+ log.error(p.format_message())
+ raise PartitionFinderError
+
+ except ParseException, p:
+ log.error("""There was a problem loading your .cfg file, please
+ check and try again""")
+ log.error(str(p))
+
+ # Let's see if there was something missing from the input file
+ expectations = ["models", "search", "[schemes]", "[data_blocks]",
+ "model_selection", "branchlengths", "alignment"]
+ missing = None
+ for e in expectations:
+ if p.msg.count(e):
+ missing = e
+
+ if missing:
+ log.info(
+ """It looks like the '%s' option might be missing or in the
+ wrong place. Or perhaps something is wrong in the lines just
+ before the '%s' option is missing. Please double check the
+ configuration file and try again""" % (missing, missing))
+ else:
+ log.info(
+ """The line causing the problem is this: '%s'. Please
+ check that line, and make sure it appears in the right
+ place in the config file. If it looks OK, try
+ double-checking the semi-colons on other lines""" % p.line)
+ raise PartitionFinderError
+
+ def set_models(self, text, loc, tokens):
+ mods = tokens[1:]
+
+ log.info("You set 'models' to: %s" % ', '.join(mods))
+
+ mods = list(mods)
+
+ self.cfg.models = [x.upper() for x in mods]
+
+ mo.load_models(self.cfg)
+ self.cfg.model_count = len(self.cfg.models)
+
+
+
+
diff --git a/partfinder/phyml.py b/partfinder/phyml.py
new file mode 100644
index 0000000..5a2800d
--- /dev/null
+++ b/partfinder/phyml.py
@@ -0,0 +1,226 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import sys
+import util
+
+from pyparsing import (
+ Word, Literal, nums, Suppress, ParseException,
+ SkipTo,
+)
+
+import phyml_models as models
+from database import DataRecord, DataLayout
+
+_binary_name = 'phyml'
+if sys.platform == 'win32':
+ _binary_name += ".exe"
+_phyml_binary = None
+
+def make_data_layout(cfg):
+ return DataLayout()
+
+
+def run_phyml(command):
+ global _phyml_binary
+ if _phyml_binary is None:
+ _phyml_binary = util.find_program(_binary_name)
+ util.run_program(_phyml_binary, command)
+
+
+def make_topology(alignment_path, datatype, cmdline_extras):
+ '''Make a BioNJ tree to start the analysis'''
+ log.info("Making BioNJ tree for %s", alignment_path)
+ cmdline_extras = check_defaults(cmdline_extras)
+
+ # First get the BioNJ topology like this:
+ if datatype == "DNA":
+ command = "-i '%s' -o n -b 0 %s" % (alignment_path, cmdline_extras)
+ elif datatype == "protein":
+ command = "-i '%s' -o n -b 0 -d aa %s" % (
+ alignment_path, cmdline_extras)
+ else:
+ log.error("Unrecognised datatype: '%s'" % (datatype))
+ raise util.PartitionFinderError
+
+ run_phyml(command)
+ output_path = make_tree_path(alignment_path)
+ return output_path
+
+
+def make_branch_lengths(alignment_path, topology_path, datatype, cmdline_extras):
+ # Now we re-estimate branchlengths using a GTR+I+G model on the
+ # (unpartitioned) dataset
+ cmdline_extras = check_defaults(cmdline_extras)
+ dir_path, fname = os.path.split(topology_path)
+ tree_path = os.path.join(dir_path, 'topology_tree.phy')
+ log.debug("Copying %s to %s", topology_path, tree_path)
+ util.dupfile(topology_path, tree_path)
+
+ if datatype == "DNA":
+ log.info("Estimating GTR+I+G branch lengths on tree")
+ command = "-i '%s' -u '%s' -m GTR -c 4 -a e -v e -o lr -b 0 %s" % (
+ alignment_path, tree_path, cmdline_extras)
+ run_phyml(command)
+ if datatype == "protein":
+ log.info("Estimating LG+F branch lengths on tree")
+ command = "-i '%s' -u '%s' -m LG -c 1 -v 0 -f m -d aa -o lr -b 0 %s" % (
+ alignment_path, tree_path, cmdline_extras)
+ run_phyml(command)
+
+ tree_path = make_tree_path(alignment_path)
+ log.info("Branchlength estimation finished")
+
+ # Now return the path of the final tree alignment
+ return tree_path
+
+
+def check_defaults(cmdline_extras):
+ """We use some sensible defaults, but allow users to override them with
+ extra cmdline options"""
+
+ if cmdline_extras.count("--min_diff_lk_global") > 0:
+ accuracy_global = ""
+ else:
+ accuracy_global = " --min_diff_lk_global 0.01 "
+ if cmdline_extras.count("--min_diff_lk_local") > 0:
+ accuracy_local = ""
+ else:
+ accuracy_local = " --min_diff_lk_local 0.01 "
+
+ # Turn off any memory checking in PhyML - thanks Jess Thomas for pointing out this problem
+ no_mem = "--no_memory_check"
+
+ # We'll put spaces at the start and end too, just in case...
+ cmdline_extras = ''.join(
+ [" ", cmdline_extras, accuracy_local, accuracy_global, no_mem, " "])
+
+
+ return cmdline_extras
+
+
+def analyse(model, alignment_path, tree_path, branchlengths, cmdline_extras):
+ """Do the analysis -- this will overwrite stuff!"""
+
+ # Move it to a new name to stop phyml stomping on different model analyses
+ # dupfile(alignment_path, analysis_path)
+ model_params = models.get_model_commandline(model)
+
+ if branchlengths == 'linked':
+ #constrain all branchlengths to be equal
+ bl = ' --constrained_lens '
+ elif branchlengths == 'unlinked':
+ #let branchlenghts vary among subsets
+ bl = ''
+ else:
+ # WTF?
+ log.error("Unknown option for branchlengths: %s", branchlengths)
+ raise util.PartitionFinderError
+
+ cmdline_extras = check_defaults(cmdline_extras)
+
+ command = "--run_id %s -b 0 -i '%s' -u '%s' %s %s %s " % (
+ model, alignment_path, tree_path, model_params, bl, cmdline_extras)
+ run_phyml(command)
+
+ # Now get rid of this -- we have the original elsewhere
+ # os.remove(analysis_path)
+
+
+def make_tree_path(alignment_path):
+ pth, ext = os.path.splitext(alignment_path)
+ return pth + ".phy_phyml_tree"
+
+
+def make_output_path(aln_path, model):
+ # analyse_path = os.path.join(root_path, name + ".phy")
+ pth, ext = os.path.splitext(aln_path)
+ stats_path = "%s.phy_phyml_stats_%s" % (pth, model)
+ tree_path = "%s.phy_phyml_tree_%s" % (pth, model)
+ return stats_path, tree_path
+
+
+def remove_files(aln_path, model):
+ '''remove all files from the alignment directory that are produced by phyml'''
+ fnames = make_output_path(aln_path, model)
+ util.delete_files(fnames)
+
+
+class PhymlResult(DataRecord):
+ pass
+
+
+class Parser(object):
+ def __init__(self, cfg):
+ self.cfg = cfg
+ FLOAT = Word(nums + '.-').setParseAction(lambda x: float(x[0]))
+ INTEGER = Word(nums + '-').setParseAction(lambda x: int(x[0]))
+
+ OB = Suppress("(")
+ CB = Suppress(")")
+ LNL_LABEL = Literal("Log-likelihood:")
+ TREE_SIZE_LABEL = Literal("Tree size:")
+ TIME_LABEL = Literal("Time used:")
+ HMS = Word(nums + "hms") # A bit rough...
+
+ lnl = (LNL_LABEL + FLOAT("lnl"))
+ tree_size = (TREE_SIZE_LABEL + FLOAT("tree_size"))
+ time = (TIME_LABEL + HMS(
+ "time") + OB + INTEGER("seconds") + Suppress("seconds") + CB)
+
+ # Shorthand...
+ def nextbit(label, val):
+ return Suppress(SkipTo(label)) + val
+
+ # Just look for these things
+ self.root_parser = \
+ nextbit(LNL_LABEL, lnl) +\
+ nextbit(TREE_SIZE_LABEL, tree_size) +\
+ nextbit(TIME_LABEL, time)
+
+ def parse(self, text):
+ log.debug("Parsing phyml output...")
+ try:
+ tokens = self.root_parser.parseString(text)
+ except ParseException, p:
+ log.error(str(p))
+ raise util.ParseError
+
+ log.debug("Parsed LNL: %s" % tokens.lnl)
+ log.debug("Parsed TREESIZE: %s" % tokens.tree_size)
+ log.debug("Parsed TIME: %s" % tokens.time)
+
+ res = PhymlResult(self.cfg)
+ res.lnl = tokens.lnl
+ res.site_rate = tokens.tree_size
+ res.seconds = tokens.seconds
+
+ return res
+
+
+def parse(text, cfg):
+ the_parser = Parser(cfg)
+ return the_parser.parse(text)
+
+
+def fabricate(lnl):
+ result = PhymlResult(lnl, 0, 0)
+ return result
diff --git a/partfinder/phyml_models.py b/partfinder/phyml_models.py
new file mode 100644
index 0000000..6073a64
--- /dev/null
+++ b/partfinder/phyml_models.py
@@ -0,0 +1,72 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it
+# under the terms of the GNU General Public License as published by the
+# Free Software Foundation, either version 3 of the License, or (at your
+# option) any later version.
+#
+# This program is distributed in the hope that it will be useful, but
+# WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+# General Public License for more details. You should have received a copy
+# of the GNU General Public License along with this program. If not, see
+#<http://www.gnu.org/licenses/>. PartitionFinder also includes the PhyML
+# program, the RAxML program, and the PyParsing library,
+# all of which are protected by their own licenses and conditions, using
+# PartitionFinder implies that you agree with those licences and
+# conditions as well.
+
+import logtools
+from util import memoize
+from config import the_config
+from model_utils import get_num_params
+log = logtools.get_logger()
+
+
+ at memoize
+def get_model_difficulty(modelstring):
+ """
+ Input a model string like HKY+I+G or LG+G+F, and a guess about how long it
+ takes to analyse Right now, this is done with a simple hack. I just return
+ a number that is the number of params plus a modifier for extra stuff like
+ +I and +G the hardest models are +I+G, then +G, then +I this is just used
+ to rank models for ordering the analysis. The return is a 'difficulty'
+ score that can be used to rank models for queing and do the hardest first
+ """
+
+ elements = modelstring.split("+")
+
+ model_params = get_num_params(modelstring)
+
+ difficulty = 0
+ if "G" in elements[1:]:
+ difficulty += 2000
+ if "I" in elements[1:]:
+ difficulty += 1000
+ if "F" in elements[1:]:
+ difficulty += 3000
+ if "X" in elements[1:]:
+ difficulty += 4000
+
+ if the_config.datatype == "protein" and "GTR" in modelstring:
+ # that's a tough model with 189 free parameters
+ difficulty += 10000
+
+ extras = modelstring.count("+")
+ total = model_params + extras + difficulty
+ log.debug("Model: %s Difficulty: %d" % (modelstring, total))
+
+ return total
+
+
+ at memoize
+def get_model_commandline(modelstring):
+ """
+ Input a model string, and get the PhyML command line
+ """
+
+ commandline = the_config.available_models.query("name=='%s'" % modelstring).phyml_commandline.values[0]
+ return commandline
+
+if __name__ == "__main__":
+ pass
diff --git a/partfinder/progress.py b/partfinder/progress.py
new file mode 100644
index 0000000..9c208d7
--- /dev/null
+++ b/partfinder/progress.py
@@ -0,0 +1,84 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+class Progress(object):
+ def __init__(self, cfg):
+ self.cfg = cfg
+ self.cfg.progress = self
+
+ def begin(self, scheme_count, subset_count):
+ pass
+
+ def next_scheme(self):
+ pass
+
+ def subset_begin(self, sub):
+ pass
+
+ def subset_done(self, sub):
+ pass
+
+ def end(self):
+ pass
+
+
+class NoProgress(Progress):
+ pass
+
+
+class TextProgress(Progress):
+
+ def begin(self, scheme_count, subset_count):
+ self.scheme_count = scheme_count
+ self.subset_count = subset_count
+ self.schemes_analysed = 0
+ self.subsets_analysed = set()
+
+ if "kmeans" not in self.cfg.search:
+ if subset_count > 10000:
+ log.warning("""%d is a lot of subsets, this might take a
+ long time to analyse. Perhaps consider using a different
+ search scheme instead (see the Manual)"""
+ % subset_count)
+
+ def next_scheme(self):
+ self.schemes_analysed += 1
+ #log.info("Analysing scheme %d/%d", self.schemes_analysed,self.scheme_count)
+
+ def subset_begin(self, sub):
+ #log.info("Begin analysing subset %s", sub)
+ pass
+
+ def subset_done(self, sub):
+ old_num_done = len(self.subsets_analysed)
+ self.subsets_analysed.add(sub.subset_id)
+ num_subs_done = len(self.subsets_analysed)
+ if old_num_done != num_subs_done:
+
+ if "kmeans" in self.cfg.search:
+ pass
+ else:
+ percent_done = (
+ float(num_subs_done) * 100.0) / float(self.subset_count)
+ log.info("Finished subset %d/%d, %.2f percent done" %
+ (num_subs_done, self.subset_count, percent_done))
+
+ def end(self):
+ pass
diff --git a/partfinder/raxml.py b/partfinder/raxml.py
new file mode 100644
index 0000000..a3edb93
--- /dev/null
+++ b/partfinder/raxml.py
@@ -0,0 +1,348 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import sys
+import fnmatch
+import util
+from database import DataLayout, DataRecord
+
+from pyparsing import (
+ Word, Literal, nums, Suppress, ParseException,
+ SkipTo, OneOrMore, Regex, restOfLine, Optional
+)
+
+import raxml_models as models
+
+_protein_letters = "ARNDCQEGHILKMFPSTWYV"
+_dna_letters = "ATCG"
+
+# This is set as the binary name because the previously compiled raxml had a
+# bug when calculating site likelihoods, this needs to be changed back to
+# "raxml" once a newer version without the bug is compiled.
+_binary_name = 'raxml'
+if sys.platform == 'win32':
+ _binary_name += ".exe"
+_raxml_binary = None
+
+
+def make_data_layout(cfg):
+ if cfg.datatype == "protein":
+ letters = _protein_letters
+ elif cfg.datatype == "DNA":
+ letters = _dna_letters
+ return DataLayout(letters)
+
+
+def run_raxml(command):
+ global _raxml_binary
+ if _raxml_binary is None:
+ _raxml_binary = util.find_program(_binary_name)
+ util.run_program(_raxml_binary, command)
+
+
+def make_topology(alignment_path, datatype, cmdline_extras):
+ '''Make a MP tree to start the analysis'''
+ log.info("Making MP tree for %s", alignment_path)
+
+ cmdline_extras = check_defaults(cmdline_extras)
+
+ # First get the MP topology like this (-p is a hard-coded random number seed):
+ if datatype == "DNA":
+ command = "-y -s '%s' -m GTRGAMMA -n MPTREE -p 123456789 %s" % (
+ alignment_path, cmdline_extras)
+ elif datatype == "protein":
+ command = "-y -s '%s' -m PROTGAMMALG -n MPTREE -p 123456789 %s" % (
+ alignment_path, cmdline_extras)
+ else:
+ log.error("Unrecognised datatype: '%s'" % (datatype))
+ raise util.PartitionFinderError
+
+ # Force raxml to write to the dir with the alignment in it
+ aln_dir, fname = os.path.split(alignment_path)
+ command = ''.join([command, " -w '%s'" % os.path.abspath(aln_dir)])
+
+ run_raxml(command)
+ dir, aln = os.path.split(alignment_path)
+ tree_path = os.path.join(dir, "RAxML_parsimonyTree.MPTREE")
+
+ if not os.path.exists(tree_path):
+ log.error("RAxML tree topology should be here but can't be be found: '%s'" % (tree_path))
+ raise(RaxmlError)
+ else:
+ log.debug("RAxML tree with branch lengths ('%s') looks like this: ", tree_path)
+ with open(tree_path, 'r') as fin:
+ log.debug('%s', fin.read())
+
+ log.info("Topology estimation finished")
+
+ return tree_path
+
+
+def make_branch_lengths(alignment_path, topology_path, datatype, cmdline_extras):
+ # Now we re-estimate branchlengths using a GTR+G model on the
+ # (unpartitioned) dataset
+ cmdline_extras = check_defaults(cmdline_extras)
+ dir_path, fname = os.path.split(topology_path)
+ tree_path = os.path.join(dir_path, 'topology_tree.phy')
+ log.debug("Copying %s to %s", topology_path, tree_path)
+ util.dupfile(topology_path, tree_path)
+ os.remove(topology_path) # saves headaches later...
+
+ if datatype == "DNA":
+ log.info("Estimating GTR+G branch lengths on tree using RAxML")
+ command = "-f e -s '%s' -t '%s' -m GTRGAMMA -n BLTREE -w '%s' %s " % (
+ alignment_path, tree_path, os.path.abspath(dir_path), cmdline_extras)
+ run_raxml(command)
+ if datatype == "protein":
+ log.info("Estimating LG+G branch lengths on tree using RAxML")
+ command = "-f e -s '%s' -t '%s' -m PROTGAMMALG -n BLTREE -w '%s' %s " % (
+ alignment_path, tree_path, os.path.abspath(dir_path), cmdline_extras)
+ run_raxml(command)
+
+ dir, aln = os.path.split(alignment_path)
+ tree_path = os.path.join(dir, "RAxML_result.BLTREE")
+
+ if not os.path.exists(tree_path):
+ log.error("RAxML tree topology should be here but can't be be found: '%s'" % (tree_path))
+ raise(RaxmlError)
+ else:
+ log.debug("RAxML tree with branch lengths ('%s') looks like this: ", tree_path)
+ with open(tree_path, 'r') as fin:
+ log.debug('%s', fin.read())
+
+ log.info("Branchlength estimation finished")
+
+ # Now return the path of the final tree with branch lengths
+ return tree_path
+
+
+def check_defaults(cmdline_extras):
+ # We use some sensible defaults, but allow users to override them with
+ # extra cmdline options
+ if cmdline_extras.count("-e") > 0:
+ # then the user has specified a particular accuracy:
+ accuracy = ""
+ else:
+ # we specify a default accuracy of 1 lnL unit
+ accuracy = " -e 1.0 "
+
+ # and we'll specify the -O option, so that the program doesn't exit if
+ # there are undetermined seqs. we'll put spaces at the start and end too,
+ # just in case...
+ cmdline_extras = ''.join([" ", cmdline_extras, accuracy, "-O "])
+ return cmdline_extras
+
+
+def analyse(model, alignment_path, tree_path, branchlengths, cmdline_extras):
+ """Do the analysis -- this will overwrite stuff!"""
+
+ # Move it to a new name to stop raxml stomping on different model analyses
+ # dupfile(alignment_path, analysis_path)
+ model_params = models.get_model_commandline(model)
+
+ if branchlengths == 'linked':
+ #constrain all branchlengths to be equal
+ bl = ' -f B '
+ elif branchlengths == 'unlinked':
+ #let branchlenghts vary among subsets
+ bl = ' -f e '
+ else:
+ # WTF?
+ log.error("Unknown option for branchlengths: %s", branchlengths)
+ raise util.PartitionFinderError
+
+ cmdline_extras = check_defaults(cmdline_extras)
+
+ # we can save memory on gappy alignments like this
+ #if str(model).count('LG4')==0:
+ # cmdline_extras = ' '.join([cmdline_extras, '-U '])
+
+ #raxml doesn't append alignment names automatically, like PhyML, let's do that here
+ analysis_ID = raxml_analysis_ID(alignment_path, model)
+
+ #force raxml to write to the dir with the alignment in it
+ #-e 1.0 sets the precision to 1 lnL unit. This is all that's required here, and helps with speed.
+ aln_dir, fname = os.path.split(alignment_path)
+ command = " %s -s '%s' -t '%s' %s -n %s -w '%s' %s" % (
+ bl, alignment_path, tree_path, model_params, analysis_ID, os.path.abspath(aln_dir), cmdline_extras)
+ run_raxml(command)
+
+
+def raxml_analysis_ID(alignment_path, model):
+ dir, file = os.path.split(alignment_path)
+ aln_name = os.path.splitext(file)[0]
+ analysis_ID = '%s_%s.txt' % (aln_name, model)
+ return analysis_ID
+
+
+def make_tree_path(alignment_path):
+ dir, aln = os.path.split(alignment_path)
+ tree_path = os.path.join(dir, "RAxML_result.BLTREE")
+ return tree_path
+
+
+def make_output_path(alignment_path, model):
+ analysis_ID = raxml_analysis_ID(alignment_path, model)
+ dir, aln_file = os.path.split(alignment_path)
+ stats_fname = "RAxML_info.%s" % (analysis_ID)
+ stats_path = os.path.join(dir, stats_fname)
+ tree_fname = "RAxML_result.%s" % (analysis_ID)
+ tree_path = os.path.join(dir, tree_fname)
+ return stats_path, tree_path
+
+
+def remove_files(aln_path, model):
+ '''remove all files from the alignment directory that are produced by raxml'''
+ dir, file = os.path.split(aln_path)
+ analysis_ID = raxml_analysis_ID(aln_path, model)
+ dir = os.path.abspath(dir)
+ fs = os.listdir(dir)
+ fnames = fnmatch.filter(fs, '*%s*%s*' % ("RAxML", analysis_ID))
+
+ pths = [os.path.join(dir, p) for p in fnames]
+ util.delete_files(pths)
+
+
+class RaxmlResult(DataRecord):
+ pass
+
+
+class Parser(object):
+ def __init__(self, cfg):
+ self.cfg = cfg
+
+ if cfg.datatype == "protein":
+ letters = _protein_letters
+ elif cfg.datatype == "DNA":
+ letters = _dna_letters
+ else:
+ log.error("Unknown datatype '%s', please check" % self.cfg.datatype)
+ raise util.PartitionFinderError
+
+ self.rate_indexes = self.cfg.data_layout.rate_indexes
+ self.freq_indexes = self.cfg.data_layout.letter_indexes
+
+ FLOAT = Word(nums + '.-').setParseAction(lambda x: float(x[0]))
+
+ L = Word(letters, exact=1)
+ COLON = Suppress(":")
+
+ LNL_LABEL = Regex("Final GAMMA.+:") | Literal("Likelihood:")
+ TIME_LABEL = Regex("Overall Time.+:") | Regex("Overall Time.+tion ")
+ ALPHA_LABEL = Literal("alpha:")
+ TREE_SIZE_LABEL = Literal("Tree-Length:")
+
+ def labeled_float(label):
+ return Suppress(SkipTo(label)) + Suppress(label) + FLOAT
+
+ lnl = labeled_float(LNL_LABEL)
+ lnl.setParseAction(self.set_lnl)
+
+ seconds = labeled_float(TIME_LABEL)
+ seconds.setParseAction(self.set_seconds)
+
+ alpha = labeled_float(ALPHA_LABEL)
+ alpha.setParseAction(self.set_alpha)
+
+ tree_size = labeled_float(TREE_SIZE_LABEL)
+ tree_size.setParseAction(self.set_tree_size)
+
+ LG4X_LINE = "LG4X" + restOfLine
+ lg4x = Optional(LG4X_LINE + LG4X_LINE)
+
+ rate = Suppress("rate") + L + Suppress("<->") + L + COLON + FLOAT
+ rate.setParseAction(self.set_rate)
+ rates = OneOrMore(rate)
+
+ freq = Suppress("freq pi(") + L + Suppress("):") + FLOAT
+ freq.setParseAction(self.set_freq)
+ freqs = OneOrMore(freq)
+
+ LGM_LINE = "LGM" + restOfLine
+
+ rate_block = Optional(LGM_LINE) + rates + freqs
+ rate_block.setParseAction(self.rate_block)
+
+ # Just look for these things
+ self.root_parser = seconds + lnl + alpha + tree_size +\
+ lg4x + OneOrMore(rate_block)
+
+ def rate_block(self, tokens):
+ self.current_block += 1
+
+ def set_seconds(self, tokens):
+ self.result.seconds = tokens[0]
+
+ def set_lnl(self, tokens):
+ self.result.lnl = tokens[0]
+
+ def set_tree_size(self, tokens):
+ self.result.site_rate = tokens[0]
+
+ def set_alpha(self, tokens):
+ self.result.alpha = tokens[0]
+
+ def set_rate(self, tokens):
+ # Ignore anything after the first rate block
+ if self.current_block > 1:
+ return
+ basefrom, baseto, rate = tokens
+ index = self.rate_indexes["%s_%s" % (basefrom, baseto)]
+ self.result.rates[0, index] = rate
+
+ def set_freq(self, tokens):
+ # Ignore anything after the first rate block
+ if self.current_block > 1:
+ return
+ base, rate = tokens
+ index = self.freq_indexes[base]
+ self.result.freqs[0, index] = rate
+
+ def parse(self, text):
+ log.debug("Parsing raxml output...")
+ self.result = RaxmlResult(self.cfg)
+
+ # The LGM produces multiple blocks of frequencies. We just want the
+ # first one, so we must remember where we are.
+ self.current_block = 1
+ try:
+ self.root_parser.parseString(text)
+ except ParseException, p:
+ log.error(str(p))
+ raise util.ParseError
+
+ log.debug("Result is %s", self.result)
+ return self.result
+
+
+def parse(text, cfg):
+ the_parser = Parser(cfg)
+ return the_parser.parse(text)
+
+
+def fabricate(lnl):
+ result = Parser('DNA')
+ result.result = RaxmlResult()
+ result.result.lnl = lnl
+ result.result.tree_size = 0
+ result.result.seconds = 0
+ result.result.alpha = 0
+ return result.result
diff --git a/partfinder/raxml_models.py b/partfinder/raxml_models.py
new file mode 100644
index 0000000..5e60f86
--- /dev/null
+++ b/partfinder/raxml_models.py
@@ -0,0 +1,90 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+import model_loader as mo
+from util import memoize
+from config import the_config
+
+from model_utils import get_num_params
+log = logtools.get_logger()
+
+
+
+ at memoize
+def get_model_commandline(modelstring):
+ '''
+ Input a model string, and get the piece of the raxml command line that defines that model
+ '''
+
+ commandline = the_config.available_models.query("name=='%s'" % modelstring).raxml_commandline.values[0]
+ return commandline
+
+
+def get_model_difficulty(modelstring):
+ """
+ Input a model string like HKY+I+G or LG+G+F, and a guess about how long it
+ takes to analyse Right now, this is done with a simple hack. I just return
+ a number that is the number of params plus a modifier for extra stuff like
+ +I and +G the hardest models are +I+G, then +G, then +I this is just used
+ to rank models for ordering the analysis. The return is a 'difficulty'
+ score that can be used to rank models for queing and do the hardest first
+ """
+
+ elements = modelstring.split("+")
+
+ model_params = get_num_params(modelstring)
+
+ difficulty = 0
+ if "G" in elements[1:]:
+ difficulty += 2000
+ if "I" in elements[1:]:
+ difficulty += 1000
+ if "F" in elements[1:]:
+ difficulty += 3000
+ if "X" in elements[1:]:
+ difficulty += 4000
+
+ if the_config.datatype == "protein" and "GTR" in modelstring:
+ # that's a tough model with 189 free parameters
+ difficulty += 10000
+
+ extras = modelstring.count("+")
+ total = model_params + extras + difficulty
+ log.debug("Model: %s Difficulty: %d" % (modelstring, total))
+
+ return total
+
+if __name__ == "__main__":
+ print " ",
+ print "Name".ljust(15),
+ print "Params".ljust(10),
+ print "Diff".ljust(10),
+ print "CommandLine"
+ for i, model in enumerate(get_all_dna_models()):
+ print str(i+1).rjust(2),
+ print model.ljust(15),
+ print str(get_num_params(model)).ljust(10),
+ print str(get_model_difficulty(model)).ljust(10),
+ print get_model_commandline(model)
+ for i, model in enumerate(get_all_protein_models()):
+ print str(i+1).rjust(2),
+ print model.ljust(15),
+ print str(get_num_params(model)).ljust(10),
+ print str(get_model_difficulty(model)).ljust(10),
+ print get_model_commandline(model)
+
diff --git a/partfinder/reporter.py b/partfinder/reporter.py
new file mode 100644
index 0000000..067cf81
--- /dev/null
+++ b/partfinder/reporter.py
@@ -0,0 +1,325 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+import pandas
+log = logtools.get_logger()
+from config import the_config
+from model_utils import get_raxml_protein_modelstring
+
+
+import os
+
+scheme_header_template = "%-18s: %s\n"
+scheme_subset_template = "%-6s | %-10s | %-10s | %-32s | %-100s\n"
+subset_template = "%-15s | %-15s | %-15s | %-15s | %-15s | %-15s\n"
+
+# We write different output for these searches
+_odd_searches = ['kmeans']
+
+class TextReporter(object):
+ def __init__(self, config):
+ self.cfg = config
+ self.cfg.reporter = self
+
+ def write_subset_summary(self, sub):
+ pth = os.path.join(self.cfg.subsets_path, sub.subset_id + '.txt')
+ # Sort everything
+
+ cols = ['model_id', 'params', 'lnl', 'aicc', 'aic', 'bic']
+
+ descr = self.cfg.data_layout.data_type.descr
+ indices = dict([(t[0], i) for i, t in enumerate(descr) if t[0] in cols])
+
+ sorted_results = [(row['aicc'], row) for row in sub.result_array]
+ sorted_results.sort()
+
+
+ output = open(pth, 'w')
+ output.write("Model selection results for subset: %s\n" % sub.subset_id)
+ if sub.alignment_path:
+ output.write("Subset alignment stored here: %s\n" % sub.alignment_path)
+ if the_config.search not in _odd_searches:
+ output.write("This subset contains the following data_blocks: %s\n" % sub.name)
+ output.write("Number of columns in subset: %d\n" % len(sub.columns))
+ output.write("Models are organised according to their AICc scores\n\n")
+
+ output.write(subset_template % ("Model", "Parameters", "lNL", "AICc", "AIC", "BIC"))
+ for aicc, row in sorted_results:
+ output.write(subset_template % (row[indices['model_id']],
+ row[indices['params']],
+ row[indices['lnl']],
+ row[indices['aicc']],
+ row[indices['aic']],
+ row[indices['bic']]))
+
+
+ def write_scheme_summary(self, sch, result):
+ pth = os.path.join(self.cfg.schemes_path, sch.name + '.txt')
+ output = open(pth, 'w')
+ self.output_scheme(sch, result, output)
+
+ def output_scheme(self, sch, result, output):
+ self.write_scheme_header(sch, result, output)
+ sorted_subsets = [sub for sub in sch]
+ sorted_subsets.sort(key=lambda sub: min(sub.columns), reverse=False)
+ self.write_subsets(sch, result, output, sorted_subsets)
+ self.write_nexus_summary(output, sorted_subsets)
+ self.write_raxml(sch, result, output, sorted_subsets)
+
+ def write_scheme_header(self, sch, result, output):
+ output.write(scheme_header_template % ("Scheme Name", sch.name))
+ output.write(scheme_header_template % ("Scheme lnL", result.lnl))
+ if self.cfg.model_selection == "aic":
+ output.write(scheme_header_template % ("Scheme AIC", result.aic))
+ if self.cfg.model_selection == "aicc":
+ output.write(scheme_header_template % ("Scheme AICc", result.aicc))
+ if self.cfg.model_selection == "bic":
+ output.write(scheme_header_template % ("Scheme BIC", result.bic))
+ output.write(scheme_header_template % ("Number of params", result.sum_k))
+ output.write(scheme_header_template % ("Number of sites", result.nsites))
+ output.write(scheme_header_template % ("Number of subsets", result.nsubs))
+ output.write("\n")
+
+ def write_nexus_summary(self, output, sorted_subsets):
+ output.write("\n\nNexus formatted character sets\n")
+ output.write("begin sets;\n")
+
+ subset_number = 1
+ charpartition = []
+ for sub in sorted_subsets:
+ if self.cfg.search in _odd_searches:
+ sites = [x + 1 for x in sub.columns]
+ partition_sites = str(sites).strip('[]')
+ else:
+ partition_sites = sub.site_description
+
+ output.write("\tcharset Subset%s = %s;\n" % (subset_number, partition_sites))
+ charpartition.append("Group%s:Subset%s" % (subset_number, subset_number))
+ subset_number += 1
+ output.write('\tcharpartition PartitionFinder = %s;\n' % ', '.join(charpartition))
+ output.write('end;\n')
+
+ def write_subsets(self, sch, result, output, sorted_subsets):
+
+ output.write(scheme_subset_template % (
+ "Subset", "Best Model", "# sites", "subset id", "Partition names"))
+ number = 1
+ # a way to print out the scheme in PF format
+ pf_scheme_description = []
+
+ if self.cfg.search in _odd_searches:
+ for sub in sorted_subsets:
+ num_sites = len(sub.columns)
+
+ sites = [x + 1 for x in sub.columns]
+ pf_scheme_description.append("(%s)" % str(sites).strip('[]'))
+ output.write(scheme_subset_template % (
+ number,
+ sub.best_model,
+ num_sites,
+ sub.subset_id,
+ 'NA',
+ ))
+ number += 1
+
+ else:
+ for sub in sorted_subsets:
+ pf_scheme_description.append("(%s)" % sub.name)
+ output.write(scheme_subset_template % (
+ number,
+ sub.best_model,
+ len(sub.columns),
+ sub.subset_id,
+ sub.name,
+ ))
+ number += 1
+
+
+ pf_scheme_description = " ".join(pf_scheme_description)
+ output.write("\n\nScheme Description in PartitionFinder format\n")
+ output.write("Scheme_%s = %s;" % (sch.name, pf_scheme_description))
+
+ def write_raxml(self, sch, result, output, sorted_subsets):
+ """Print out partition definitions in RaxML-like format, might be
+ useful to some people
+ """
+ output.write("\n\nRaxML-style partition definitions\n")
+
+ subset_number = 1
+ for sub in sorted_subsets:
+ if self.cfg.search in _odd_searches:
+ sites = [x + 1 for x in sub.columns]
+ partition_sites = str(sites).strip('[]')
+ else:
+ partition_sites = sub.site_description
+
+ if self.cfg.datatype == "DNA":
+ model = 'DNA'
+ elif self.cfg.datatype == "protein":
+ model = get_raxml_protein_modelstring(sub.best_model)
+ else:
+ raise RuntimeError
+
+ output.write("%s, Subset%s = %s" % (model, subset_number, partition_sites))
+ output.write("\n")
+ subset_number += 1
+
+ output.write("\nWarning: RAxML allows for only a single model of rate"
+ " heterogeneity in partitioned analyses. I.e. all "
+ "partitions must be assigned either a +G model or a "
+ "+I+G model. If the best models for your dataset"
+ "contain both types of model, you will need to choose "
+ "an appropriate rate heterogeneity model when you run "
+ "RAxML. This is specified through the command line to "
+ "RAxML. To rigorously choose the best model, run two "
+ "further PF analyses (these will be fast), fixing "
+ "the partitioning scheme to this scheme and "
+ "'search=user;', in both. In one run, use only +I+G "
+ "models ('models = all_protein_gammaI'); in the next, "
+ "use only +G models ('models = all_protein_gamma;''). "
+ "Choose the scheme with the lowest AIC/AICc/BIC score. "
+ "Note that these re-runs will be quick!"
+ )
+
+ def write_best_scheme(self, result):
+ pth = os.path.join(self.cfg.output_path, 'best_scheme.txt')
+ output = open(pth, 'wb')
+ output.write('Settings used\n\n')
+ output.write(scheme_header_template % ("alignment", self.cfg.alignment_path))
+ output.write(scheme_header_template % ("branchlengths", self.cfg.branchlengths))
+ output.write(scheme_header_template % ("models", ', '.join(self.cfg.models)))
+ output.write(scheme_header_template % ("model_selection",
+ self.cfg.model_selection))
+ output.write(scheme_header_template % ("search", self.cfg.search))
+ if self.cfg.search in ["rcluster", "hcluster"]:
+ pretty_weights = "rate = %s, base = %s, model = %s, alpha = %s" %(
+ str(self.cfg.cluster_weights["rate"]),
+ str(self.cfg.cluster_weights["freqs"]),
+ str(self.cfg.cluster_weights["model"]),
+ str(self.cfg.cluster_weights["alpha"]))
+ output.write(scheme_header_template % ("weights", pretty_weights))
+
+ if self.cfg.search == "rcluster":
+ output.write(scheme_header_template % ("rcluster-percent",
+ self.cfg.cluster_percent))
+ output.write(scheme_header_template % ("rcluster-max",
+ self.cfg.cluster_max))
+
+ if self.cfg.search == "kmeans":
+ output.write(scheme_header_template % ("min-subset-size",
+ self.cfg.min_subset_size))
+ output.write(scheme_header_template % ("kmeans based on",
+ self.cfg.kmeans))
+ if self.cfg.all_states == True:
+ output.write(scheme_header_template % ("--all_states setting used",
+ self.cfg.all_states))
+
+
+ output.write('\n\nBest partitioning scheme\n\n')
+ self.output_scheme(result.best_scheme, result.best_result, output)
+ log.info("Information on best scheme is here: %s", pth)
+
+ citation_text = write_citation_text(self)
+
+ # now we write subset summaries for all the subsets in the best scheme
+ for s in result.best_scheme:
+ self.write_subset_summary(s)
+
+ log.info("\n")
+ log.info("\n")
+
+ for c in citation_text:
+ log.info("%s", c)
+ output.write(c)
+
+
+
+def write_citation_text(self):
+ """Tell users which papers to cite"""
+
+ citation_text = []
+
+ ref_PF2 = ("Lanfear, R., Calcott, B., Frandsen, P. Forthcoming. "
+ "PartitionFinder 2: new methods for selecting partitioning "
+ "schemes and models of molecular evolution for large datasets. "
+ "In preparation.")
+
+ ref_PF1 = ("Lanfear, R., Calcott, B., Ho, S. Y., & Guindon, S. (2012). "
+ "PartitionFinder: combined selection of partitioning schemes "
+ "and substitution models for phylogenetic analyses. "
+ "Molecular biology and evolution, 29(6), 1695-1701.")
+
+ ref_rcluster = ("Lanfear, R., Calcott, B., Kainer, D., Mayer, C., "
+ "& Stamatakis, A. (2014). Selecting optimal "
+ "partitioning schemes for phylogenomic datasets. "
+ "BMC evolutionary biology, 14(1), 82.")
+
+ ref_kmeans = ("Frandsen, P. B., Calcott, B., Mayer, C., & Lanfear, R. "
+ "(2015). Automatic selection of partitioning schemes for "
+ "phylogenetic analyses using iterative k-means clustering "
+ "of site rates. BMC Evolutionary Biology, 15(1), 13.")
+
+ ref_phyml = ("Guindon, S., Dufayard, J. F., Lefort, V., Anisimova, M., "
+ "Hordijk, W., & Gascuel, O. (2010). New algorithms and "
+ "methods to estimate maximum-likelihood phylogenies: "
+ "assessing the performance of PhyML 3.0. "
+ "Systematic biology, 59(3), 307-321.")
+
+ ref_raxml = ("Stamatakis, A. (2014). RAxML version 8: a tool for "
+ "phylogenetic analysis and post-analysis of large phylogenies. "
+ "Bioinformatics, 30(9), 1312-1313.")
+
+ citation_text.append("\n\n\n*Citations for this analysis*\n")
+ citation_text.append("-----------------------------")
+
+ citation_text.append("\n")
+
+ citation_text.append("If you use this analysis in your published "
+ "work, please cite "
+ "the following papers on which your analysis relied.\n")
+
+ citation_text.append("\n")
+ citation_text.append("For the version of PartitionFinder you used, "
+ "please cite:\n")
+
+ citation_text.append("%s\n" % ref_PF2)
+
+ citation_text.append("\n")
+ citation_text.append("For the %s algorithm you used, please cite:\n"
+ % (self.cfg.search))
+
+ if self.cfg.search == "rcluster" or self.cfg.search == "hcluster":
+ citation_text.append("%s\n" % ref_rcluster)
+
+ elif self.cfg.search == "kmeans":
+ citation_text.append("%s\n" % ref_kmeans)
+
+ elif self.cfg.search == "greedy":
+ citation_text.append("%s\n" % ref_PF1)
+
+ citation_text.append("\n")
+ if self.cfg.phylogeny_program == 'phyml':
+ citation_text.append("Your analysis also used PhyML, so please cite:\n")
+ citation_text.append("%s\n" % ref_phyml)
+
+ elif self.cfg.phylogeny_program == 'raxml':
+ citation_text.append("Your analysis also used RAxML, so please cite:\n")
+ citation_text.append("%s\n" % ref_raxml)
+ citation_text.append("\n")
+
+ return citation_text
\ No newline at end of file
diff --git a/partfinder/results.py b/partfinder/results.py
new file mode 100644
index 0000000..9939d6d
--- /dev/null
+++ b/partfinder/results.py
@@ -0,0 +1,98 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import cPickle as pickle
+
+from util import PartitionFinderError
+
+_check_fields = "lnl aic aicc bic".split()
+
+
+class ComparisonError(PartitionFinderError):
+ pass
+
+
+class AnalysisResults(object):
+ """
+ This stores the results, keeping only the winning scheme.
+ """
+
+ MAX_ERROR = .1
+
+ def __init__(self, model_selection):
+ self.model_selection = model_selection
+ self.best_score = None
+ self.best_result = None
+ self.best_scheme = None
+
+ def add_scheme_result(self, sch, result):
+ score = result.score
+ if self.best_score is None or score < self.best_score:
+ self.best_score = score
+ self.best_result = result
+ self.best_scheme = sch
+
+ def get_dump_path(self, cfg):
+ return os.path.join(cfg.base_path, 'results.bin')
+
+ def get_result_fields(self):
+ flds = []
+ for k in _check_fields:
+ flds.append(getattr(self.best_result, k))
+ return flds
+
+ def dump(self, cfg):
+ pth = self.get_dump_path(cfg)
+ log.info("Dumping all results to '%s'", pth)
+ f = open(pth, 'wb')
+ pickle.dump(self.get_result_fields(), f, -1)
+
+ def compare(self, cfg):
+ """We only compare the best result!"""
+ pth = self.get_dump_path(cfg)
+ if not os.path.exists(pth):
+ log.error("Previous results file not found at '%s'. "
+ "Did you run --dump-results previously?", pth)
+ raise ComparisonError
+
+ log.info("Loading old results from '%s'", pth)
+ f = open(pth, 'rb')
+ old_fields = pickle.load(f)
+ f.close()
+
+ cur_fields = self.get_result_fields()
+
+ log.info("Comparing results...")
+ # Now do the comparison
+
+ errors = 0
+ for nm, oldv, curv in zip(_check_fields, old_fields, cur_fields):
+ if abs(oldv - curv) > self.MAX_ERROR:
+ log.error("Differences were more than acceptable value of %s", AnalysisResults.MAX_ERROR)
+ log.error("Old %s value: %s, new %s value %s", nm, oldv, nm, curv)
+ errors += 1
+
+ if errors > 0:
+ raise ComparisonError
+ else:
+ log.info(
+ "All results were within an acceptable %s of the dumped results",
+ AnalysisResults.MAX_ERROR)
diff --git a/partfinder/scheme.py b/partfinder/scheme.py
new file mode 100644
index 0000000..1c3f751
--- /dev/null
+++ b/partfinder/scheme.py
@@ -0,0 +1,239 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import subset_ops
+import submodels
+
+from util import PartitionFinderError, get_aic, get_aicc, get_bic
+
+
+class SchemeError(PartitionFinderError):
+ pass
+
+
+class SchemeResult(object):
+ def __init__(self, sch, nseq, branchlengths, model_selection):
+ self.scheme_name = sch.name
+ self.scheme = sch
+ self.model_selection = model_selection
+
+ # Calculate AIC, BIC, AICc for each scheme.
+ # How you do this depends on whether brlens are linked or not.
+ self.nsubs = len(sch.subsets) # number of subsets
+ sum_subset_k = sum([s.best_params for s in sch]) # sum of number of parameters in the best model of each subset
+
+ log.debug("""Calculating number of parameters in scheme.
+ Total parameters from subset models: %d""" % (sum_subset_k))
+
+ if branchlengths == 'linked': # linked brlens - only one extra parameter per subset
+ self.sum_k = sum_subset_k + (self.nsubs - 1) + (
+ (2 * nseq) - 3) # number of parameters in a scheme
+ log.debug("Total parameters from brlens: %d" %
+ ((2 * nseq) - 3))
+ log.debug("Parameters from subset multipliers: %d" %
+ (self.nsubs - 1))
+
+ elif branchlengths == 'unlinked': # unlinked brlens - every subset has its own set of brlens
+ self.sum_k = sum_subset_k + (self.nsubs * (
+ (2 * nseq) - 3)) # number of parameters in a scheme
+ log.debug("Total parameters from brlens: %d" % ((
+ 2 * nseq) - 3) * self.nsubs)
+
+ else:
+ # WTF?
+ log.error("Unknown option for branchlengths: %s", branchlengths)
+ raise PartitionFinderError
+
+ log.debug("Grand total parameters: %d" % (self.sum_k))
+
+ self.lnl = sum([s.best_lnl for s in sch])
+ self.nsites = sum([len(s.column_set) for s in sch])
+
+ K = float(self.sum_k)
+ n = float(self.nsites)
+ lnL = float(self.lnl)
+
+ log.debug("n: %d\tK: %d\tlnL: %d" % (n, K, lnL))
+
+ self.aic = get_aic(lnL, K)
+ self.bic = get_bic(lnL, K, n)
+ self.aicc = get_aicc(lnL, K, n)
+
+ @property
+ def score(self):
+ return getattr(self, self.model_selection)
+
+ def __repr__(self):
+ return "SchemeResult<score({0.model_selection}):{0.score}>".format(self)
+
+
+class Scheme(object):
+ def __init__(self, cfg, name, subsets, description=None):
+ """A set of subsets of partitions"""
+ self.name = name
+ self.subsets = set(subsets)
+ self.description = description
+
+ # TODO: Fix this!
+ if subset_ops.subsets_overlap(subsets):
+ log.error("Scheme '%s' contains overlapping subsets", name)
+ raise SchemeError
+ #
+ #if subset_ops.has_missing(subsets):
+ # log.error("Scheme '%s' has missing subsets", name)
+ # raise SchemeError
+ #
+ #log.debug("Created %s" % self)
+
+ def __iter__(self):
+ return iter(self.subsets)
+
+ def __str__(self):
+ ss = ', '.join([str(s) for s in self.subsets])
+ return "Scheme(%s, %s)" % (self.name, ss)
+
+ def get_fabricated_subsets(self):
+ fabricated_subsets = []
+ for sub in self.subsets:
+ if sub.fabricated:
+ fabricated_subsets.append(sub)
+ return fabricated_subsets
+
+
+class SchemeSet(object):
+ """All the schemes added, and also a list of all unique subsets"""
+ def __init__(self):
+ """A collection of schemes"""
+ self.clear_schemes()
+
+ def clear_schemes(self):
+ self.schemes_by_name = {}
+ # self.schemes_by_subsets = {}
+
+ def add_scheme(self, scheme):
+ if scheme.name in self.schemes_by_name:
+ log.error("Cannot add two schemes with same name: '%s'" %
+ scheme.name)
+ raise SchemeError
+
+ # TODO: Recheck schemes to make sure they're ok...
+ # if scheme.part_subsets in self.schemes_by_subsets:
+ # existing_scheme = \
+ # self.schemes_by_subsets[scheme.part_subsets]
+ # log.warning(
+ # "Scheme named %s being added is identical to existing %s",
+ # scheme.name, existing_scheme)
+ # # raise SchemeError
+
+ self.schemes_by_name[scheme.name] = scheme
+ # self.schemes_by_subsets[scheme.part_subsets] = scheme
+
+ def __len__(self):
+ return len(self.schemes_by_name)
+
+ def __iter__(self):
+ return iter(self.schemes_by_name.itervalues())
+
+
+def create_scheme(cfg, scheme_name, scheme_description):
+ """
+ Generate a single scheme given a list of numbers that represent the
+ indexes of the partitions e.g. [0,1,2,3,4,5,6,7]
+ """
+
+ subset_count = len(cfg.user_subsets)
+
+ # Check that the correct number of items are in the list
+ if len(scheme_description) != subset_count:
+ log.error("There's a problem with the description of scheme %s" %
+ scheme_name)
+ raise SchemeError
+
+ # Now generate the pattern
+ subs = {}
+ # We use the numbers returned to group the different subsets
+ for sub_index, grouping in enumerate(scheme_description):
+ insub = subs.setdefault(grouping, [])
+ insub.append(sub_index)
+
+ # We now have what we need to create a subset. Each entry will have a
+ # set of values which are the index for the partition
+ created_subsets = []
+ for sub_indexes in subs.values():
+ subs_to_merge = [cfg.user_subsets[i] for i in sub_indexes]
+ sub = subset_ops.merge_subsets(subs_to_merge)
+ created_subsets.append(sub)
+
+ return Scheme(cfg, str(scheme_name), created_subsets, description=scheme_description)
+
+
+def model_to_scheme(model, scheme_name, cfg):
+ """Turn a model definition e.g. [0, 1, 2, 3, 4] into a scheme"""
+ subs = {}
+ # We use the numbers returned to group the different subsets
+ for sub_index, grouping in enumerate(model):
+ insub = subs.setdefault(grouping, [])
+ insub.append(sub_index)
+
+ # We now have what we need to create a subset. Each entry will have a
+ # set of values which are the index for the partition
+ created_subsets = []
+ for sub_indexes in subs.values():
+ subs_to_merge = [cfg.user_subsets[i] for i in sub_indexes]
+ sub = subset_ops.merge_subsets(subs_to_merge)
+ created_subsets.append(sub)
+
+ return Scheme(cfg, str(scheme_name), created_subsets)
+
+
+def generate_all_schemes(cfg):
+ """
+ Convert the abstract schema given by the algorithm into subsets
+ """
+
+ log.info("Generating all possible schemes for the partitions...")
+
+ subset_count = len(cfg.user_subsets)
+
+ # Now generate the pattern for this many partitions
+ all_schemes = submodels.get_submodels(subset_count)
+ scheme_name = 1
+ scheme_list = []
+ for scheme in all_schemes:
+ subs = {}
+ # We use the numbers returned to group the different subsets
+ for sub_index, grouping in enumerate(scheme):
+ insub = subs.setdefault(grouping, [])
+ insub.append(sub_index)
+ # We now have what we need to create a subset. Each entry will have a
+ # set of values which are the index for the partition
+ created_subsets = []
+ for sub_indexes in subs.values():
+ sub = subset_ops.merge_subsets(
+ [cfg.user_subsets[i] for i in sub_indexes])
+ created_subsets.append(sub)
+
+ scheme_list.append(Scheme(cfg, str(scheme_name), created_subsets))
+
+ log.debug("Created scheme %d of %d" % (scheme_name, len(all_schemes)))
+
+ scheme_name += 1
+
+ return scheme_list
diff --git a/partfinder/submodels.py b/partfinder/submodels.py
new file mode 100644
index 0000000..c613b29
--- /dev/null
+++ b/partfinder/submodels.py
@@ -0,0 +1,159 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import math
+
+def submodel_generator(result, pat, current, maxn):
+ """ result is a list to append to
+ pat is the current pattern (starts as empty list)
+ current is the current number of the pattern
+ maxn is the number of items in the pattern
+ """
+ if pat:
+ curmax = max(pat)
+ else:
+ curmax = 0
+ for i in range(current):
+ if i-1 <= curmax:
+ newpat = pat[:]
+ newpat.append(i)
+ if current == maxn:
+ result.append(newpat)
+ else:
+ submodel_generator(result, newpat, current+1, maxn)
+
+def submodel_iterator(pat, current, maxn):
+ """same as generator but yields instead"""
+ if pat:
+ curmax = max(pat)
+ else:
+ curmax = 0
+ for i in range(current):
+ if i-1 <= curmax:
+ newpat = pat[:]
+ newpat.append(i)
+ if current == maxn:
+ yield newpat
+ else:
+ for b in submodel_iterator(newpat, current+1, maxn):
+ yield b
+
+def a_choose_b(n,k):
+ return reduce(lambda a,b: a*(n-b)/(b+1),xrange(k),1)
+
+def count_relaxed_clustering_subsets(N, cluster_percent, cluster_max):
+ #startscheme
+ start_scheme = N
+ #firstbatch is just cluster_percent of N choose 2
+ step_1 = int(math.ceil(a_choose_b(N, 2)*cluster_percent*0.01))
+ if cluster_max != None and step_1>cluster_max:
+ step_1 = cluster_max
+ previous = step_1
+ cumsum = start_scheme+step_1
+
+ #now for the rest
+ for i in reversed(xrange(N)):
+
+ # once we get to the all combined scheme we can stop
+ if i == 1:
+ break
+ num_new_schemes = int(math.ceil((a_choose_b(i, 2))*cluster_percent*0.01))
+ # but those new schemes include a lot we will have already analysed
+ # so we want to subtract that many. We could have already seen up to i-1 choose 2
+ # the worst case is that the scheme we chose knocked out the maximum number of
+ # previously analysed schemes, which is just 2(i)-1, so:
+ worst_case = 2*i - 1
+ num_already_analysed = previous - worst_case
+ # now we transfer over the 'previous' for the next round of the loop
+ previous = num_new_schemes
+ # now we calculate the final number of new schemes
+ num_new_schemes -= num_already_analysed
+ if cluster_max != None and num_new_schemes>cluster_max:
+ num_new_schemes = cluster_max
+ cumsum += num_new_schemes
+
+ return cumsum
+
+def count_relaxed_clustering_schemes(N, cluster_percent, cluster_max):
+ #startscheme
+ start_scheme = 1
+ #firstbatch is just cluster_percent of N choose 2
+ step_1 = int(math.ceil(a_choose_b(N, 2)*cluster_percent*0.01))
+
+ if cluster_max != None and step_1>cluster_max:
+ step_1 = cluster_max
+
+ cumsum = start_scheme+step_1
+ #now for the rest
+ for i in reversed(xrange(N)):
+ # each subsequent step is cluster_percent of i choose 2
+ if i == 1:
+ break
+ num_new_schemes = int(math.ceil((a_choose_b(i, 2))*cluster_percent*0.01))
+ if cluster_max != None and num_new_schemes>cluster_max:
+ num_new_schemes = cluster_max
+ cumsum += num_new_schemes
+ return cumsum
+
+def count_greedy_schemes(N):
+ """oeis.org reveals this is 1+(N*(N+1)*(N-1))/6"""
+ count = 1+(N*(N+1)*(N-1))/6
+ return count
+
+def count_greedy_subsets(N):
+ """oeis.org says thes are Central polygonal numbers: n^2 - n + 1. """
+ count = (N*N) - N + 1
+ return count
+
+def bell_numbers(N):
+ ## Return the bell number for N subsets
+ # script modified from Wikipedia: http://en.wikipedia.org/wiki/Bell_number
+ N += 1## Bell numbers are indexed from zero
+ t = [[1]] ## Initialize the triangle as a two-dimensional array
+ c = 1 ## Bell numbers count
+ while c <= N:
+ if c >= N:
+ return t[-1][0] ## Yield the Bell number of the previous row
+ row = [t[-1][-1]] ## Initialize a new row
+ for b in t[-1]:
+ row.append(row[-1] + b) ## Populate the new row
+ c += 1 ## We have found another Bell number
+ t.append(row) ## Append the row to the triangle
+
+
+def get_submodels(N):
+ """Return all the submodels
+ """
+ log.debug("Generating submodels for %s partitions", N)
+ result = []
+ submodel_generator(result, [], 1, N)
+ log.debug("Resulting number of partitions is %s", len(result))
+ return result
+
+def count_all_schemes(N):
+ """Count the number of submodels we"ve got"""
+ count = bell_numbers(N)
+ return count
+
+def count_all_subsets(N):
+ """Count the number of subses we'll have to look at given a certain number of starting partitions"""
+ count = (2**N) - 1
+ return count
+
diff --git a/partfinder/subset.py b/partfinder/subset.py
new file mode 100644
index 0000000..a4a1a93
--- /dev/null
+++ b/partfinder/subset.py
@@ -0,0 +1,360 @@
+# Copyright (C) 2012-2013 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import numpy
+
+from alignment import Alignment, SubsetAlignment
+from util import (ParseError, PartitionFinderError, remove_runID_files, get_aic, get_aicc,
+ get_bic)
+import subset_ops
+
+
+FRESH, PREPARED, DONE = range(3)
+
+
+class SubsetError(PartitionFinderError):
+ pass
+
+
+def count_subsets():
+ return len(Subset._cache)
+
+
+def clear_subsets():
+ Subset._cache.clear()
+
+
+class Subset(object):
+ """Contains a set of columns in the Alignment
+ """
+ _cache = {}
+
+ def __new__(cls, cfg, column_set, name=None, description=None):
+ """Returns the identical subset if the columns are identical.
+
+ This is basically a pythonized factory. See here:
+ http://codesnipers.com/?q=python-flyweights
+ """
+ columns = list(column_set)
+ columns.sort()
+ subset_id = subset_ops.subset_unique_name(columns)
+ obj = Subset._cache.get(subset_id, None)
+ if not obj:
+ obj = object.__new__(cls)
+ Subset._cache[subset_id] = obj
+ obj.init(subset_id, cfg, column_set, columns)
+
+ return obj
+
+ def init(self, subset_id, cfg, column_set, columns):
+ self.subset_id = subset_id
+ self.cfg = cfg
+ self.column_set = column_set
+ self.columns = columns
+ self.status = FRESH
+ self.names = []
+ self.description = []
+
+ # We put all results into this array, which is sized to the number of
+ # models that we are analysing
+ self.result_array = numpy.zeros(
+ cfg.model_count, cfg.data_layout.data_type)
+
+ # This points to the current empty array entry that we will fill up
+ # next. When we're done it will equal the size of the array (and
+ # accessing will cause an error)
+ self.result_current = 0
+
+ # This will get set to the best entry, once we've done all the analysis
+ self.result_best = None
+
+ self.models_not_done = set(cfg.models)
+
+ self.fabricated = False
+ self.dont_split = False
+ self.analysis_error = None
+ self.centroid = None
+
+ # Site likelihoods calculated using GTR+G from the
+ # processor.gen_per_site_stats()
+ self.site_lnls_GTRG = []
+
+ self.alignment_path = None
+ log.debug("Created %s" % self)
+
+ def add_description(self, names, description):
+ """User created subsets can get some extra info"""
+ self.names = names
+ self.description = description
+
+ @property
+ def name(self):
+ try:
+ return ", ".join(self.names)
+ except:
+ return "NA"
+
+ @property
+ def site_description(self):
+ try:
+ s = []
+ for desc in self.description:
+ step = desc[2]
+ if step == 1:
+ text = "%s-%s" % (desc[0], desc[1])
+ else:
+ text = "%s-%s\\%s" % tuple(desc)
+ s.append(text)
+ site_description = ', '.join(s)
+ return site_description
+ except:
+ return ', '.join(map(str, self.columns))
+
+ def __repr__(self):
+ return "Subset(%s..)" % self.name[:5]
+
+ def load_results(self, cfg):
+ matching = cfg.database.get_results_for_subset(self)
+ # We might get models that we don't want, so we need to filter them
+ for i, mod in enumerate(matching['model_id']):
+ if mod in self.models_not_done:
+ self.result_array[self.result_current] = matching[i]
+ self.result_current += 1
+ self.models_not_done.remove(mod)
+
+ def add_result(self, cfg, model, result):
+ """
+ We get the result class from raxml or phyml. We need to transform this
+ into a numpy record, and then store it locally, and in the database
+ """
+ K = float(cfg.processor.models.get_num_params(model))
+ n = float(len(self.column_set))
+ lnL = float(result.lnl)
+ aic = get_aic(lnL, K)
+ bic = get_bic(lnL, K, n)
+ aicc = get_aicc(lnL, K, n)
+
+ result.subset_id = self.subset_id
+ result.model_id = model
+ result.params = K
+ result.aic = aic
+ result.aicc = aicc
+ result.bic = bic
+
+ # Now assign the data record in the result into the current model
+ # result and save it to the database
+ self.result_array[self.result_current] = result._data
+ cfg.database.save_result(self, self.result_current)
+ self.result_current += 1
+
+ log.debug("Added model to subset. Model: %s, params: %d, sites:%d, lnL:%.2f, site_rate %f"
+ % (model, K, n, lnL, result.site_rate))
+
+ def model_selection(self, cfg):
+ # We want the index of the smallest value
+ method = cfg.model_selection
+ self.result_best = numpy.argmin(self.result_array[method])
+ best = self.result_array[self.result_best]
+
+ # TODO: this is crappy. Anyone who wants this stuff should just access
+ # the entire "best" item
+ self.best_info_score = best[method]
+ self.best_lnl = best['lnl']
+ self.best_model = best['model_id']
+ self.best_site_rate = best['site_rate']
+ self.best_params = best['params']
+ self.best_alpha = best['alpha']
+ self.best_freqs = best['freqs']
+ self.best_rates = best['rates']
+
+ log.debug("Best model for this subset: %s \n"
+ "lnL: %s\n"
+ "site_rate: %s\n"
+ "params: %s\n"
+ "alpha: %s\n"
+ "freqs: %s\n"
+ "rates: %s\n"
+ % (self.best_model, str(self.best_lnl),
+ str(self.best_site_rate), str(self.best_params),
+ str(self.best_alpha), str(self.best_freqs),
+ str(self.best_rates)))
+
+ def get_param_values(self):
+ param_values = {
+ "rate": self.best_site_rate,
+ "model": self.best_rates,
+ "alpha": self.best_alpha,
+ "freqs": self.best_freqs,
+ }
+ return param_values
+
+
+
+ def finalise(self, cfg):
+ if self.models_not_done:
+ return False
+
+ # We might already have done everything
+ if self.status == DONE:
+ return True
+
+ self.model_selection(cfg)
+
+ # Do all the final cleanup
+ if cfg.save_phylofiles:
+ # Write out a summary of the subsets
+ cfg.reporter.write_subset_summary(self)
+ else:
+ # Otherwise, clean up files generated by the programs as well
+ if self.alignment_path:
+ remove_runID_files(self.alignment_path)
+
+ self.models_to_process = []
+ self.status = DONE
+ cfg.progress.subset_done(self)
+ return True
+
+ def prepare(self, cfg, alignment):
+ """Get everything ready for running the analysis
+ """
+ cfg.progress.subset_begin(self)
+
+ # Load the cached results
+ self.load_results(cfg)
+ if self.finalise(cfg):
+ return
+
+ # Make an Alignment from the source, using this subset
+ self.make_alignment(cfg, alignment)
+ self.models_to_process = list(self.models_not_done)
+ # Now order them by difficulty
+ self.models_to_process.sort(
+ key=cfg.processor.models.get_model_difficulty,
+ reverse=True)
+
+ self.status = PREPARED
+
+ def parse_results(self, cfg):
+ """Read in the results and parse them"""
+ for m in list(self.models_not_done):
+ self.parse_model_result(cfg, m)
+
+ def fabricate_model_result(self, cfg, model):
+ self.fabricated = True
+ self.dont_split = True
+ self.models_not_done.remove(model)
+
+ def parse_model_result(self, cfg, model):
+ pth, tree_path = cfg.processor.make_output_path(
+ self.alignment_path, model)
+
+ if not os.path.exists(pth):
+ # If it ain't there, we can't do it
+ return
+
+ output = open(pth, 'rb').read()
+ try:
+ result = cfg.processor.parse(output, cfg)
+ self.add_result(cfg, model, result)
+ # Remove the current model from remaining ones
+ self.models_not_done.remove(model)
+
+ if not cfg.save_phylofiles:
+ # We remove all files that have the specified RUN ID
+ cfg.processor.remove_files(self.alignment_path, model)
+
+ except ParseError:
+ # If we're loading old files, this is fine
+ if self.status == FRESH:
+ log.warning("Failed loading parse output from %s."
+ "Output maybe corrupted. I'll run it again.",
+ pth)
+ cfg.processor.remove_files(self.alignment_path, model)
+ else:
+ # But if we're prepared, then we've just run this. And we're
+ # screwed. Reraise the message
+ log.error(
+ "Failed to run models %s; not sure why",
+ ", ".join(list(self.models_not_done)))
+ raise
+
+ def add_per_site_statistics(self, per_site_stats):
+ self.site_lnls = per_site_stats
+
+ def fabricate_result(self, cfg, model):
+ '''If the subset fails to be analyzed, we throw some "fabricated"
+ results'''
+ processor = cfg.processor
+ self.fabricated = True
+
+ lnl = sum(self.site_lnls_GTRG)
+ result = processor.fabricate(lnl)
+
+ self.add_result(cfg, model, result)
+ self.best_params = cfg.processor.models.get_num_params(model)
+ self.best_lnl = result.lnl
+ self.models_not_done.remove(model)
+
+ def add_centroid(self, centroid):
+ self.centroid = centroid
+
+ FORCE_RESTART_MESSAGE = """
+ It looks like you have changed one or more of the data_blocks in the
+ configuration file, so the new subset alignments don't match the ones
+ stored for this analysis. You'll need to run the program with
+ --force-restart
+ """
+
+ def make_alignment(self, cfg, alignment):
+ # Make an Alignment from the source, using this subset
+ sub_alignment = SubsetAlignment(alignment, self)
+
+ sub_path = os.path.join(cfg.phylofiles_path, self.subset_id + '.phy')
+ # Add it into the sub, so we keep it around
+ self.alignment_path = sub_path
+
+ # Maybe it is there already?
+ if os.path.exists(sub_path):
+ log.debug("Found existing alignment file %s" % sub_path)
+ old_align = Alignment()
+ old_align.read(sub_path)
+
+ # It had better be the same!
+ if not old_align.same_as(sub_alignment):
+ log.error(self.FORCE_RESTART_MESSAGE)
+ raise SubsetError
+ else:
+ # We need to write it
+ sub_alignment.write(sub_path)
+
+ @property
+ def is_done(self):
+ return self.status == DONE
+
+ @property
+ def is_prepared(self):
+ return self.status == PREPARED
+
+ @property
+ def is_fresh(self):
+ return self.status == FRESH
+
+
diff --git a/partfinder/subset_ops.py b/partfinder/subset_ops.py
new file mode 100644
index 0000000..bbca763
--- /dev/null
+++ b/partfinder/subset_ops.py
@@ -0,0 +1,195 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import hashlib
+import cPickle as pickle
+import subset
+from util import get_aic, get_aicc, get_bic
+from scipy.stats import chi2
+
+def columnset_to_string(colset):
+ s = list(colset)
+ s.sort()
+ # Add one, cos we converted to zero base...
+ return ', '.join([str(x+1) for x in s])
+
+def subset_unique_name(columns):
+ """Return a unique string based on the subsets columns (which are unique)"""
+
+ # Use pickle to give us a string from the object
+ pickled_columns = pickle.dumps(columns, -1)
+
+ # Now get an md5 hash from this. There is some vanishingly small chance that
+ # we'll get the same thing. Google "MD5 Hash Collision"
+ return hashlib.md5(pickled_columns).hexdigest()
+
+def merge_fabricated_subsets(subset_list):
+ '''Allows the merging of fabricated subsets and the preservation of their
+ centroids and lnls'''
+ columns = set()
+ lnl = 0
+ centroid = []
+
+ # Figure out how many dimensions the centroid is
+ centroid_dim = len(subset_list[0].centroid)
+ for i in range(centroid_dim):
+ centroid.append(0)
+
+ for sub in subset_list:
+ columns |= sub.column_set
+ lnl += sub.best_lnl
+ number = 0
+ for observation in centroid:
+ observation += sub.centroid[number]
+ number += 1
+
+ # Now just take the average of each centroid to be the centroid of the new
+ # subset
+ centroid = [x/len(subset_list) for x in centroid]
+
+ new_sub = subset.Subset(sub.cfg, columns)
+
+ # Add the centroid and sum of the lnls to the subset. TODO: create
+ # functions to update these variables in the subset rather than messing
+ # with them directly
+ new_sub.centroid = centroid
+ new_sub.lnl = lnl
+ return new_sub
+
+
+def merge_subsets(subset_list):
+ """Take a set of subsets and merge them together"""
+ columns = set()
+
+ # We just need the columns
+ names = []
+ descriptions = []
+ for sub in subset_list:
+ columns |= sub.column_set
+ descriptions.extend(sub.description)
+ names.extend(sub.names)
+
+ newsub = subset.Subset(sub.cfg, columns)
+ # Only add the description if it isn't there (we might get back a cache
+ # hit)
+ if not newsub.names:
+ newsub.add_description(names, descriptions)
+
+ return newsub
+
+def subsets_overlap(subset_list):
+ columns = set()
+ overlapping = []
+
+ for sub in subset_list:
+ # If the intersection is non-empty...
+ ov = list(sub.column_set & columns)
+ if ov:
+ overlapping.append(ov)
+ columns |= sub.column_set
+
+ return ov
+
+def check_against_alignment(full_subset, alignment):
+ """Check the subset definition against the alignment"""
+
+ alignment_set = set(range(0, alignment.sequence_length))
+ leftout = alignment_set - full_subset.column_set
+ if leftout:
+ # This does not raise an error, just a warning
+ log.warning(
+ "These columns are missing from the block definitions: %s",
+ columnset_to_string(leftout))
+
+
+def split_subset(a_subset, cluster_list):
+ """Takes a subset and splits it according to a cluster list,
+ then returns the subsets resulting from the split"""
+ # Take each site from the first list and add it to a new
+ subset_list = a_subset.columns
+ subset_columns = []
+ list_of_subsets = []
+ for cluster in cluster_list:
+ list_of_sites = []
+ for site in cluster:
+ list_of_sites.append(subset_list[site - 1])
+ subset_columns.append(set(list_of_sites))
+
+ tracker = 0
+ for column_set in subset_columns:
+ new_subset = subset.Subset(a_subset.cfg, column_set)
+ list_of_subsets.append(new_subset)
+ tracker += 1
+
+ return list_of_subsets
+
+def subset_list_score(list_of_subsets, the_config, alignment):
+ """Takes a list of subsets and return the aic, aicc, or bic score"""
+
+ lnL, sum_k, subs_len = subset_list_stats(list_of_subsets, the_config, alignment)
+
+ if the_config.model_selection == 'aic':
+ return get_aic(lnL, sum_k)
+ elif the_config.model_selection == 'aicc':
+ return get_aicc(lnL, sum_k, subs_len)
+ elif the_config.model_selection == 'bic':
+ return get_bic(lnL, sum_k, subs_len)
+
+
+def subset_list_stats(list_of_subsets, the_config, alignment):
+ """Takes a list of subsets and returns the lnL and the number of params"""
+ sum_subset_k = 0
+ lnL = 0
+ subs_len = 0
+ for sub in list_of_subsets:
+ sum_subset_k += sub.best_params
+ lnL += sub.best_lnl
+ subs_len += len(sub.columns)
+ # Grab the number of species so we know how many params there are
+ num_taxa = len(alignment.species)
+ # Linked brlens - only one extra parameter per subset
+ if the_config.branchlengths == 'linked':
+ sum_k = sum_subset_k + (len(list_of_subsets) - 1) + (
+ (2 * num_taxa) - 3)
+ log.debug("Total parameters from brlens: %d" %
+ ((2 * num_taxa) - 3))
+ log.debug("Parameters from subset multipliers: %d" %
+ (len(list_of_subsets) -1))
+
+ # Unlinked brlens - every subset has its own set of brlens
+ elif the_config.branchlengths == 'unlinked':
+ sum_k = sum_subset_k + (len(list_of_subsets) * (
+ (2 * num_taxa) - 3))
+ log.debug("Total parameters from brlens: %d" % ((
+ 2 * num_taxa) - 3) * (len(list_of_subsets)))
+
+ log.debug("Grand_total_parameters: %d", sum_k)
+
+ return lnL, sum_k, subs_len
+
+
+def subset_list_score_diff(list1, list2, the_config, alignment):
+ """Take two lists of subsets and return the score diff as list1 - list2"""
+ list1_score = subset_list_score(list1, the_config, alignment)
+ list2_score = subset_list_score(list2, the_config, alignment)
+
+ score_diff = list1_score - list2_score
+
+ return score_diff
\ No newline at end of file
diff --git a/partfinder/threadpool.py b/partfinder/threadpool.py
new file mode 100644
index 0000000..17a3527
--- /dev/null
+++ b/partfinder/threadpool.py
@@ -0,0 +1,121 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+#
+# This code modified and vastly simplified from here
+# http://code.activestate.com/recipes/203871/
+
+import logtools
+log = logtools.get_logger()
+
+import threading
+from time import sleep
+import multiprocessing
+
+_cpus = None
+
+def get_cpu_count():
+ global _cpus
+ if _cpus is not None:
+ return _cpus
+
+ try:
+ _cpus = multiprocessing.cpu_count()
+ except NotImplementedError:
+ _cpus = 1
+ log.warning('I cannot detect the number of processors...')
+ log.info("Using %s cpus", _cpus)
+
+ return _cpus
+
+
+class Pool(object):
+ def __init__(self, tasks, numthreads=-1):
+ """Initialize the thread pool with numthreads workers and all tasks"""
+ self.more_tasks = True
+ self.tasks = tasks
+ self.task_lock = threading.Condition(threading.Lock())
+ self.threads = []
+ self.failed = False
+
+ numtasks = len(tasks)
+ if numtasks == 0:
+ log.warning("You did not give any tasks to do...")
+ self.more_tasks = False
+ return
+
+ if numthreads <= 1:
+ numthreads = get_cpu_count()
+ if numtasks < numthreads:
+ numthreads = numtasks
+
+ log.debug("Creating %s threads for %s tasks", numthreads, numtasks)
+ for i in range(numthreads):
+ t = Thread(self)
+ self.threads.append(t)
+ t.start()
+
+ def next_task(self):
+ self.task_lock.acquire()
+ try:
+ if not self.tasks:
+ self.more_tasks = False
+ return None, None
+ else:
+ return self.tasks.pop(0)
+ finally:
+ self.task_lock.release()
+
+ def kill(self, e):
+ self.task_lock.acquire()
+ self.tasks = []
+ self.more_tasks = False
+ self.failed = True
+ self.exception = e
+ self.task_lock.release()
+
+ def join(self):
+ # TODO: I don't think we need this bit....
+ # Wait till all tasks have been taken
+ while self.more_tasks:
+ sleep(.1)
+ # ... now wait for them all to finish
+ for t in self.threads:
+ t.join()
+
+ if self.failed:
+ raise self.exception
+
+
+class Thread(threading.Thread):
+ def __init__(self, pool):
+ threading.Thread.__init__(self)
+ self.pool = pool
+
+ def run(self):
+ while 1:
+ cmd, args = self.pool.next_task()
+ # If there's nothing to do, return
+ if cmd is None:
+ break
+ try:
+ cmd(*args)
+ except Exception as e:
+ # The error should already have been reported.
+ # Stop operation and kill the entire pool. Then reraise the
+ # error
+ self.pool.kill(e)
+ break
diff --git a/partfinder/util.py b/partfinder/util.py
new file mode 100644
index 0000000..834b251
--- /dev/null
+++ b/partfinder/util.py
@@ -0,0 +1,223 @@
+# Copyright (C) 2012 Robert Lanfear and Brett Calcott
+#
+# This program is free software: you can redistribute it and/or modify it under
+# the terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+#
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
+# details. You should have received a copy of the GNU General Public License
+# along with this program. If not, see <http://www.gnu.org/licenses/>.
+# PartitionFinder also includes the PhyML program, the RAxML program, and the
+# PyParsing library, all of which are protected by their own licenses and
+# conditions, using PartitionFinder implies that you agree with those licences
+# and conditions as well.
+
+import logtools
+log = logtools.get_logger()
+
+import os
+import fnmatch
+import subprocess
+import shlex
+import shutil
+from math import log as logarithm
+
+
+# Base error class
+class PartitionFinderError(Exception):
+ pass
+
+class ExternalProgramError(PartitionFinderError):
+ def __init__(self, stderr, stdout):
+ self.stderr = stderr
+ self.stdout = stdout
+
+class ParseError(PartitionFinderError):
+ pass
+
+NO_CONFIG_ERROR = """
+Failed to find configuration file: '%s'. For PartitionFinder to run, there
+must be a file called 'partition_finder.cfg' located in the same folder as
+your alignment. Please check and try again.
+"""
+
+
+def find_program(binary_name):
+ """Locate the binary ..."""
+ pth = os.path.abspath(__file__)
+
+ # Split off the name and the directory...
+ pth, notused = os.path.split(pth)
+ pth, notused = os.path.split(pth)
+ pth = os.path.join(pth, "programs", binary_name)
+ pth = os.path.normpath(pth)
+
+ log.debug("Checking for program %s", binary_name)
+ if not os.path.exists(pth) or not os.path.isfile(pth):
+ log.error("No such file: '%s'", pth)
+ raise PartitionFinderError
+ log.debug("Found program %s at '%s'", binary_name, pth)
+ return pth
+
+
+def run_program(binary, command):
+ # Add in the command file
+ log.debug("Running '%s %s'", binary, command)
+ command = "\"%s\" %s" % (binary, command)
+
+ # Note: We use shlex.split as it does a proper job of handling command
+ # lines that are complex
+ p = subprocess.Popen(
+ shlex.split(command),
+ shell=False,
+ stdout=subprocess.PIPE,
+ stderr=subprocess.PIPE)
+
+ # Capture the output, we might put it into the errors
+ stdout, stderr = p.communicate()
+ # p.terminate()
+
+ if p.returncode != 0:
+ raise ExternalProgramError(stdout, stderr)
+
+def dupfile(src, dst):
+ # Make a copy or a symlink so that we don't overwrite different model runs
+ # of the same alignment
+
+ # TODO maybe this should throw...?
+ try:
+ if os.path.exists(dst):
+ os.remove(dst)
+ shutil.copyfile(src, dst)
+ except OSError:
+ log.error("Cannot link/copy file %s to %s", src, dst)
+ raise PartitionFinderError
+
+def check_file_exists(pth):
+ if not os.path.exists(pth) or not os.path.isfile(pth):
+ if pth.count("partition_finder.cfg") > 0:
+ log.error(NO_CONFIG_ERROR, pth)
+ raise PartitionFinderError
+ else:
+ log.error(
+ "Failed to find file: '%s'. Please check and try again.", pth)
+ raise PartitionFinderError
+
+
+def delete_files(pths):
+ """Delete files from paths
+
+ Watch out for a WindowsError that crops up sometimes with threading oddly,
+ this error occurs, but the files get deleted anyway. So we ignore it for
+ now
+ """
+ for f in pths:
+ try:
+ os.remove(f)
+ except OSError:
+ log.debug("Found and ignored Error when deleting file %s" % f)
+ pass
+ log.debug("deleted %d files" % len(pths))
+
+
+def check_folder_exists(pth):
+ if not os.path.exists(pth) or not os.path.isdir(pth):
+ log.error("No such folder: '%s'", pth)
+ raise PartitionFinderError
+
+
+def clean_out_folder(folder, keep=[]):
+ """Hat Tip:
+ http://stackoverflow.com/questions/185936/delete-folder-contents-in-python
+ """
+ for the_file in os.listdir(folder):
+ if the_file not in keep:
+ file_path = os.path.join(folder, the_file)
+ try:
+ if os.path.isfile(file_path):
+ os.unlink(file_path)
+ except Exception as e:
+ log.error(e)
+ raise PartitionFinderError
+
+
+def make_dir(pth):
+ if os.path.exists(pth):
+ if not os.path.isdir(pth):
+ log.error("Cannot create folder '%s'", pth)
+ raise PartitionFinderError
+ else:
+ os.mkdir(pth)
+
+
+def remove_runID_files(aln_pth):
+ """Remove all files that match a particular run_ID.
+
+ Useful for cleaning out directories but ONLY after a whole analysis of a
+ subset is completely finished, be careful!
+ """
+ head, tail = os.path.split(aln_pth)
+ run_ID = os.path.splitext(tail)[0]
+ head = os.path.abspath(head)
+ fnames = os.listdir(head)
+ fs = fnmatch.filter(fnames, '*%s*' % run_ID)
+ for f in fs:
+ try:
+ os.remove(os.path.join(head, f))
+ except OSError:
+ # Don't complain if you can't delete them (This is here because we
+ # sometimes try and delete things twice in the threading).
+ pass
+
+def memoize(f):
+ """Cache results from functions"""
+ cache = {}
+
+ def memf(*x):
+ if x not in cache:
+ cache[x] = f(*x)
+ return cache[x]
+ return memf
+
+def get_aic(lnL, K):
+ aic = (-2.0 * lnL) + (2.0 * K)
+ return aic
+
+def get_aicc(lnL, K, n):
+ SMALL_WARNING = """
+ You are calculating an AICc value in which the number of parameters
+ is large with respect to the number of sites in the alignment. Please
+ proceed with caution.
+ """
+ if n < (K + 2):
+ log.debug(SMALL_WARNING)
+ n = K + 2
+
+ aicc = (-2.0 * lnL) + ((2.0 * K) * (n / (n - K - 1.0)))
+ return aicc
+
+def get_bic(lnL, K, n):
+ bic = (-2.0 * lnL) + (K * logarithm(n))
+ return bic
+
+
+
+# def we_are_frozen():
+ # All of the modules are built-in to the interpreter, e.g., by py2exe
+ # return hasattr(sys, "frozen")
+
+# def get_root_install_path():
+ # pth = os.path.abspath(__file__)
+ # Split off the name and the directory...
+ # pth, not_used = os.path.split(pth)
+ # pth, not_used = os.path.split(pth)
+ # return pth
+
+# def module_path():
+ # encoding = sys.getfilesystemencoding()
+ # if we_are_frozen():
+ # return os.path.dirname(unicode(sys.executable, encoding))
+ # return os.path.abspath(os.path.dirname(unicode(__file__, encoding)))
diff --git a/programs/fast_TIGER b/programs/fast_TIGER
new file mode 100755
index 0000000..3888276
Binary files /dev/null and b/programs/fast_TIGER differ
diff --git a/programs/phyml b/programs/phyml
new file mode 100755
index 0000000..395aced
Binary files /dev/null and b/programs/phyml differ
diff --git a/programs/phyml.exe b/programs/phyml.exe
new file mode 100644
index 0000000..2664c28
Binary files /dev/null and b/programs/phyml.exe differ
diff --git a/programs/raxml b/programs/raxml
new file mode 100755
index 0000000..856f5bc
Binary files /dev/null and b/programs/raxml differ
diff --git a/programs/raxml.exe b/programs/raxml.exe
new file mode 100644
index 0000000..7fe8c3f
Binary files /dev/null and b/programs/raxml.exe differ
diff --git a/programs/raxml_develop b/programs/raxml_develop
new file mode 100755
index 0000000..562e7c9
Binary files /dev/null and b/programs/raxml_develop differ
diff --git a/programs/raxml_rob_SSE3_gcc b/programs/raxml_rob_SSE3_gcc
new file mode 100755
index 0000000..42c2875
Binary files /dev/null and b/programs/raxml_rob_SSE3_gcc differ
diff --git a/programs/raxml_rob_SSE3_mac b/programs/raxml_rob_SSE3_mac
new file mode 100755
index 0000000..562e7c9
Binary files /dev/null and b/programs/raxml_rob_SSE3_mac differ
diff --git a/programs/raxml_rob_gcc b/programs/raxml_rob_gcc
new file mode 100755
index 0000000..1fdeb4d
Binary files /dev/null and b/programs/raxml_rob_gcc differ
diff --git a/quick_tests.sh b/quick_tests.sh
new file mode 100644
index 0000000..f69f937
--- /dev/null
+++ b/quick_tests.sh
@@ -0,0 +1 @@
+py.test -v -k "not full" -x
diff --git a/tests/PF2/__init__.py b/tests/PF2/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/PF2/missing-sites-warning/Als_etal_2004.phy b/tests/PF2/missing-sites-warning/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/PF2/missing-sites-warning/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/PF2/missing-sites-warning/partition_finder.cfg b/tests/PF2/missing-sites-warning/partition_finder.cfg
new file mode 100644
index 0000000..b0ddaeb
--- /dev/null
+++ b/tests/PF2/missing-sites-warning/partition_finder.cfg
@@ -0,0 +1,13 @@
+alignment = Als_etal_2004.phy;
+branchlengths = linked;
+models = WAG;
+model_selection = BIC;
+
+[data_blocks]
+COI = 4-407;
+COII = 408-624;
+EF1a = 625-940;
+
+[schemes]
+search = greedy;
+
diff --git a/tests/PF2/overlapping-blocks/Als_etal_2004.phy b/tests/PF2/overlapping-blocks/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/PF2/overlapping-blocks/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/PF2/overlapping-blocks/partition_finder.cfg b/tests/PF2/overlapping-blocks/partition_finder.cfg
new file mode 100644
index 0000000..828e36d
--- /dev/null
+++ b/tests/PF2/overlapping-blocks/partition_finder.cfg
@@ -0,0 +1,13 @@
+alignment = Als_etal_2004.phy;
+branchlengths = linked;
+models = WAG;
+model_selection = BIC;
+
+[data_blocks]
+COI = 1-407;
+COII = 408-625;
+EF1a = 625-949;
+
+[schemes]
+search = greedy;
+
diff --git a/tests/PF2/test_pf2.py b/tests/PF2/test_pf2.py
new file mode 100644
index 0000000..aa24415
--- /dev/null
+++ b/tests/PF2/test_pf2.py
@@ -0,0 +1,36 @@
+"""New tests for PF2"""
+import os
+import inspect
+from partfinder import main
+import pytest
+from partfinder.util import PartitionFinderError
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+# Far too clever function
+def path_from_function():
+ funname = inspect.stack()[1][3]
+ # remove test_
+ funname = funname[5:]
+ funname = funname.replace('_', '-')
+ pth = os.path.join(HERE, funname)
+ return pth
+
+# ---------------- SUCCESS ---------------------
+
+
+# ---------------- ERRORS ---------------------
+# Check the exception, and then look in the log output for specific
+# details of the exception.
+
+def test_missing_sites_warning(caplog):
+ main.call_main("protein", '"%s"' % path_from_function())
+ assert "These columns are missing from the block definitions" in caplog.text()
+
+
+def test_overlapping_blocks(caplog):
+ with pytest.raises(PartitionFinderError):
+ main.call_main("protein", '"%s"' % path_from_function())
+ assert "following sites overlap" in caplog.text()
+
+
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/cfg/__init__.py b/tests/cfg/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/cfg/test01.cfg b/tests/cfg/test01.cfg
new file mode 100644
index 0000000..491c6a9
--- /dev/null
+++ b/tests/cfg/test01.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linKeD;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = ALl;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BiC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = UsER;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test02.cfg b/tests/cfg/test02.cfg
new file mode 100644
index 0000000..706d064
--- /dev/null
+++ b/tests/cfg/test02.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = all;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test03.cfg b/tests/cfg/test03.cfg
new file mode 100644
index 0000000..8f3eed7
--- /dev/null
+++ b/tests/cfg/test03.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = mrbayes;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test04.cfg b/tests/cfg/test04.cfg
new file mode 100644
index 0000000..7813936
--- /dev/null
+++ b/tests/cfg/test04.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = allx;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test05.cfg b/tests/cfg/test05.cfg
new file mode 100644
index 0000000..b4a29b7
--- /dev/null
+++ b/tests/cfg/test05.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = allx;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test06.cfg b/tests/cfg/test06.cfg
new file mode 100644
index 0000000..ab8a80a
--- /dev/null
+++ b/tests/cfg/test06.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = allx;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = AIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test07.cfg b/tests/cfg/test07.cfg
new file mode 100644
index 0000000..47df34b
--- /dev/null
+++ b/tests/cfg/test07.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = allx;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = AICc;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test08.cfg b/tests/cfg/test08.cfg
new file mode 100644
index 0000000..9507cda
--- /dev/null
+++ b/tests/cfg/test08.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = mrbayes;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = AICc;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = all;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test09.cfg b/tests/cfg/test09.cfg
new file mode 100644
index 0000000..5832857
--- /dev/null
+++ b/tests/cfg/test09.cfg
@@ -0,0 +1,42 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = beast;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = AICc;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = greedy;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
diff --git a/tests/cfg/test10.cfg b/tests/cfg/test10.cfg
new file mode 100644
index 0000000..1f3dc75
--- /dev/null
+++ b/tests/cfg/test10.cfg
@@ -0,0 +1,30 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = test.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = JC, TVM+I+G, HKY+G, HKY+I+G, GTR, GTR+I+G;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = AIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = all;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
diff --git a/tests/cfg/test11.cfg b/tests/cfg/test11.cfg
new file mode 100644
index 0000000..422b6b8
--- /dev/null
+++ b/tests/cfg/test11.cfg
@@ -0,0 +1,24 @@
+# Test that we can have an optional topology
+#
+alignment = test.phy;
+# user_tree_topology = top.phy;
+
+branchlengths = unlinked;
+
+models = GTR+G, GTR;
+model_selection = AICc;
+
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+[schemes]
+search = greedy;
+
diff --git a/tests/cfg/test12.cfg b/tests/cfg/test12.cfg
new file mode 100644
index 0000000..47adb97
--- /dev/null
+++ b/tests/cfg/test12.cfg
@@ -0,0 +1,26 @@
+# Fail: lack of schemes
+#
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+schemes
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/cfg/test13.cfg b/tests/cfg/test13.cfg
new file mode 100644
index 0000000..eab14ff
--- /dev/null
+++ b/tests/cfg/test13.cfg
@@ -0,0 +1,27 @@
+# Pass: Multiple lines for alignment
+#
+## ALIGNMENT FILE ##
+alignment =
+Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/cfg/test14.cfg b/tests/cfg/test14.cfg
new file mode 100644
index 0000000..e2bcfc6
--- /dev/null
+++ b/tests/cfg/test14.cfg
@@ -0,0 +1,25 @@
+# FAIL: branchlengths is mispelled
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = umlinked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+schemes
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/cfg/test15.cfg b/tests/cfg/test15.cfg
new file mode 100644
index 0000000..42f1e79
--- /dev/null
+++ b/tests/cfg/test15.cfg
@@ -0,0 +1,28 @@
+# Branch lengths in wrong place
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/cfg/test16.cfg b/tests/cfg/test16.cfg
new file mode 100644
index 0000000..9441a4a
--- /dev/null
+++ b/tests/cfg/test16.cfg
@@ -0,0 +1,25 @@
+# Model selection incorrect
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = AIC, BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/cfg/test_configs.py b/tests/cfg/test_configs.py
new file mode 100644
index 0000000..eb99a4c
--- /dev/null
+++ b/tests/cfg/test_configs.py
@@ -0,0 +1,52 @@
+import os
+import pytest
+from partfinder import util, config
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+
+def get_file_list(strlist):
+ return ["test%02d.cfg" % int(n) for n in strlist.split()]
+
+all_tests = {
+ "DNA_success": get_file_list("1 2 3 4 5 6 7 8 9 10 11"),
+ "DNA_failure": get_file_list("14"),
+ "prot_success": get_file_list("13"),
+ "prot_failure": get_file_list("12 15 16"),
+}
+
+
+def pytest_generate_tests(metafunc):
+ # This function feeds the output of the above function into the tests below
+ for c in all_tests:
+ if c in metafunc.fixturenames:
+ metafunc.parametrize(c, all_tests[c])
+
+
+def do_success(ftype, fname):
+ pth = os.path.join(HERE, fname)
+ c = config.init(datatype=ftype)
+ c.load(pth)
+
+
+def do_failure(ftype, fname):
+ pth = os.path.join(HERE, fname)
+ c = config.init(datatype=ftype)
+ with pytest.raises(util.PartitionFinderError):
+ c.load(pth)
+
+
+def test_DNA_success(DNA_success):
+ do_success("DNA", DNA_success)
+
+
+def test_DNA_failure(DNA_failure):
+ do_failure("DNA", DNA_failure)
+
+
+def test_protein_success(prot_success):
+ do_success("protein", prot_success)
+
+
+def test_protein_failure(prot_failure):
+ do_failure("protein", prot_failure)
diff --git a/tests/christof/__init__.py b/tests/christof/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/christof/alignment-error/Als_etal_2004.phy b/tests/christof/alignment-error/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/alignment-error/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/alignment-error/partition_finder.cfg b/tests/christof/alignment-error/partition_finder.cfg
new file mode 100755
index 0000000..f8f6e06
--- /dev/null
+++ b/tests/christof/alignment-error/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949 950-1000;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/clustering-phyml-dna/partition_finder.cfg b/tests/christof/clustering-phyml-dna/partition_finder.cfg
new file mode 100755
index 0000000..c7aaf07
--- /dev/null
+++ b/tests/christof/clustering-phyml-dna/partition_finder.cfg
@@ -0,0 +1,30 @@
+## ALIGNMENT FILE ##
+alignment = test.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = hcluster;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/clustering-phyml-dna/test.phy b/tests/christof/clustering-phyml-dna/test.phy
new file mode 100755
index 0000000..91e3c40
--- /dev/null
+++ b/tests/christof/clustering-phyml-dna/test.phy
@@ -0,0 +1,5 @@
+4 2208
+spp1 CTTGAGGTTCAGAATGGTAATGAA------GTGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCCATGGGTTCTTCCGACGGTCTGCGTCGCGGTCTGGATGTAAAAGACCTCGAGCACCCGATCGAAGTCCCAGTTGGTAAAGCAACACTGGGTCGTATCATGAACGTACTGGGTCAGCCAGTAGACATGAAGGGCGACATCGGTGAAGAAGAGCGTTGGGCT---------------ATCCACCGTGAAGCACCATCCTATGAAGAGCTGTCAAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTTGCGAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTTATTCGTAACATCGCGATCGAGCACTCCGGTTATTCTGTGTTTGCGGGCGTAGGTGAACGT [...]
+spp2 CTTGAGGTACAAAATGGTAATGAG------AGCCTGGTGCTGGAAGTTCAGCAGCAGCTCGGTGGTGGTATCGTACGTGCTATCGCCATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTTAAAGACCTTGAGCACCCGATCGAAGTCCCGGTTGGTAAAGCAACGCTGGGTCGTATCATGAACGTGCTGGGTCAGCCGATCGATATGAAAGGCGACATCGGCGAAGAAGAACGTTGGGCG---------------ATTCACCGTGCAGCACCTTCCTATGAAGAGCTCTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTCGCGAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTTGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAACACTCCGGTTACTCCGTGTTTGCTGGTGTTGGTGAGCGT [...]
+spp3 CTTGAGGTACAGAATAACAGCGAG------AAGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCAATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTGAAAGACCTCGAGCACCCGATCGAAGTCCCGGTAGGTAAAGCGACCCTGGGTCGTATCATGAACGTGCTGGGTCAGCCAATCGATATGAAAGGCGACATCGGCGAAGAAGATCGTTGGGCG---------------ATTCACCGCGCAGCACCTTCCTATGAAGAGCTGTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATTTGTCCGTTCGCTAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGCGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAGCACTCCGGTTACTCCGTGTTTGCAGGCGTGGGTGAGCGT [...]
+spp4 CTCGAGGTGAAAAATGGTGATGCT------CGTCTGGTGCTGGAAGTTCAGCAGCAGCTGGGTGGTGGCGTGGTTCGTACCATCGCCATGGGTACTTCTGACGGCCTGAAGCGCGGTCTGGAAGTTACCGACCTGAAAAAACCTATCCAGGTTCCGGTTGGTAAAGCAACCCTCGGCCGTATCATGAACGTATTGGGTGAGCCAATCGACATGAAAGGCGACCTGCAGAATGACGACGGCACTGTAGTAGAGGTTTCCTCTATTCACCGTGCAGCACCTTCGTATGAAGATCAGTCTAACTCGCAGGAACTGCTGGAAACCGGCATCAAGGTTATCGACCTGATGTGTCCGTTCGCTAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGGCTGAGCACTCAGGTTATTCGGTATTTGCTGGTGTGGGTGAGCGT [...]
diff --git a/tests/christof/clustering-raxml-dna/partition_finder.cfg b/tests/christof/clustering-raxml-dna/partition_finder.cfg
new file mode 100755
index 0000000..c7aaf07
--- /dev/null
+++ b/tests/christof/clustering-raxml-dna/partition_finder.cfg
@@ -0,0 +1,30 @@
+## ALIGNMENT FILE ##
+alignment = test.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = hcluster;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/clustering-raxml-dna/test.phy b/tests/christof/clustering-raxml-dna/test.phy
new file mode 100755
index 0000000..91e3c40
--- /dev/null
+++ b/tests/christof/clustering-raxml-dna/test.phy
@@ -0,0 +1,5 @@
+4 2208
+spp1 CTTGAGGTTCAGAATGGTAATGAA------GTGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCCATGGGTTCTTCCGACGGTCTGCGTCGCGGTCTGGATGTAAAAGACCTCGAGCACCCGATCGAAGTCCCAGTTGGTAAAGCAACACTGGGTCGTATCATGAACGTACTGGGTCAGCCAGTAGACATGAAGGGCGACATCGGTGAAGAAGAGCGTTGGGCT---------------ATCCACCGTGAAGCACCATCCTATGAAGAGCTGTCAAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTTGCGAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTTATTCGTAACATCGCGATCGAGCACTCCGGTTATTCTGTGTTTGCGGGCGTAGGTGAACGT [...]
+spp2 CTTGAGGTACAAAATGGTAATGAG------AGCCTGGTGCTGGAAGTTCAGCAGCAGCTCGGTGGTGGTATCGTACGTGCTATCGCCATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTTAAAGACCTTGAGCACCCGATCGAAGTCCCGGTTGGTAAAGCAACGCTGGGTCGTATCATGAACGTGCTGGGTCAGCCGATCGATATGAAAGGCGACATCGGCGAAGAAGAACGTTGGGCG---------------ATTCACCGTGCAGCACCTTCCTATGAAGAGCTCTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTCGCGAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTTGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAACACTCCGGTTACTCCGTGTTTGCTGGTGTTGGTGAGCGT [...]
+spp3 CTTGAGGTACAGAATAACAGCGAG------AAGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCAATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTGAAAGACCTCGAGCACCCGATCGAAGTCCCGGTAGGTAAAGCGACCCTGGGTCGTATCATGAACGTGCTGGGTCAGCCAATCGATATGAAAGGCGACATCGGCGAAGAAGATCGTTGGGCG---------------ATTCACCGCGCAGCACCTTCCTATGAAGAGCTGTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATTTGTCCGTTCGCTAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGCGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAGCACTCCGGTTACTCCGTGTTTGCAGGCGTGGGTGAGCGT [...]
+spp4 CTCGAGGTGAAAAATGGTGATGCT------CGTCTGGTGCTGGAAGTTCAGCAGCAGCTGGGTGGTGGCGTGGTTCGTACCATCGCCATGGGTACTTCTGACGGCCTGAAGCGCGGTCTGGAAGTTACCGACCTGAAAAAACCTATCCAGGTTCCGGTTGGTAAAGCAACCCTCGGCCGTATCATGAACGTATTGGGTGAGCCAATCGACATGAAAGGCGACCTGCAGAATGACGACGGCACTGTAGTAGAGGTTTCCTCTATTCACCGTGCAGCACCTTCGTATGAAGATCAGTCTAACTCGCAGGAACTGCTGGAAACCGGCATCAAGGTTATCGACCTGATGTGTCCGTTCGCTAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGGCTGAGCACTCAGGTTATTCGGTATTTGCTGGTGTGGGTGAGCGT [...]
diff --git a/tests/christof/greedy-phyml-dna/partition_finder.cfg b/tests/christof/greedy-phyml-dna/partition_finder.cfg
new file mode 100755
index 0000000..f9d73c6
--- /dev/null
+++ b/tests/christof/greedy-phyml-dna/partition_finder.cfg
@@ -0,0 +1,26 @@
+## ALIGNMENT FILE ##
+alignment = test.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = JC;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/greedy-phyml-dna/test.phy b/tests/christof/greedy-phyml-dna/test.phy
new file mode 100755
index 0000000..91e3c40
--- /dev/null
+++ b/tests/christof/greedy-phyml-dna/test.phy
@@ -0,0 +1,5 @@
+4 2208
+spp1 CTTGAGGTTCAGAATGGTAATGAA------GTGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCCATGGGTTCTTCCGACGGTCTGCGTCGCGGTCTGGATGTAAAAGACCTCGAGCACCCGATCGAAGTCCCAGTTGGTAAAGCAACACTGGGTCGTATCATGAACGTACTGGGTCAGCCAGTAGACATGAAGGGCGACATCGGTGAAGAAGAGCGTTGGGCT---------------ATCCACCGTGAAGCACCATCCTATGAAGAGCTGTCAAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTTGCGAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTTATTCGTAACATCGCGATCGAGCACTCCGGTTATTCTGTGTTTGCGGGCGTAGGTGAACGT [...]
+spp2 CTTGAGGTACAAAATGGTAATGAG------AGCCTGGTGCTGGAAGTTCAGCAGCAGCTCGGTGGTGGTATCGTACGTGCTATCGCCATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTTAAAGACCTTGAGCACCCGATCGAAGTCCCGGTTGGTAAAGCAACGCTGGGTCGTATCATGAACGTGCTGGGTCAGCCGATCGATATGAAAGGCGACATCGGCGAAGAAGAACGTTGGGCG---------------ATTCACCGTGCAGCACCTTCCTATGAAGAGCTCTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTCGCGAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTTGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAACACTCCGGTTACTCCGTGTTTGCTGGTGTTGGTGAGCGT [...]
+spp3 CTTGAGGTACAGAATAACAGCGAG------AAGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCAATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTGAAAGACCTCGAGCACCCGATCGAAGTCCCGGTAGGTAAAGCGACCCTGGGTCGTATCATGAACGTGCTGGGTCAGCCAATCGATATGAAAGGCGACATCGGCGAAGAAGATCGTTGGGCG---------------ATTCACCGCGCAGCACCTTCCTATGAAGAGCTGTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATTTGTCCGTTCGCTAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGCGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAGCACTCCGGTTACTCCGTGTTTGCAGGCGTGGGTGAGCGT [...]
+spp4 CTCGAGGTGAAAAATGGTGATGCT------CGTCTGGTGCTGGAAGTTCAGCAGCAGCTGGGTGGTGGCGTGGTTCGTACCATCGCCATGGGTACTTCTGACGGCCTGAAGCGCGGTCTGGAAGTTACCGACCTGAAAAAACCTATCCAGGTTCCGGTTGGTAAAGCAACCCTCGGCCGTATCATGAACGTATTGGGTGAGCCAATCGACATGAAAGGCGACCTGCAGAATGACGACGGCACTGTAGTAGAGGTTTCCTCTATTCACCGTGCAGCACCTTCGTATGAAGATCAGTCTAACTCGCAGGAACTGCTGGAAACCGGCATCAAGGTTATCGACCTGATGTGTCCGTTCGCTAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGGCTGAGCACTCAGGTTATTCGGTATTTGCTGGTGTGGGTGAGCGT [...]
diff --git a/tests/christof/greedy-phyml-protein/Als_etal_2004.phy b/tests/christof/greedy-phyml-protein/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/greedy-phyml-protein/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/greedy-phyml-protein/partition_finder.cfg b/tests/christof/greedy-phyml-protein/partition_finder.cfg
new file mode 100755
index 0000000..5ef4a9c
--- /dev/null
+++ b/tests/christof/greedy-phyml-protein/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = JTT;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/greedy-raxml-dna/partition_finder.cfg b/tests/christof/greedy-raxml-dna/partition_finder.cfg
new file mode 100755
index 0000000..e29cc6e
--- /dev/null
+++ b/tests/christof/greedy-raxml-dna/partition_finder.cfg
@@ -0,0 +1,30 @@
+## ALIGNMENT FILE ##
+alignment = test.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/greedy-raxml-dna/test.phy b/tests/christof/greedy-raxml-dna/test.phy
new file mode 100755
index 0000000..91e3c40
--- /dev/null
+++ b/tests/christof/greedy-raxml-dna/test.phy
@@ -0,0 +1,5 @@
+4 2208
+spp1 CTTGAGGTTCAGAATGGTAATGAA------GTGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCCATGGGTTCTTCCGACGGTCTGCGTCGCGGTCTGGATGTAAAAGACCTCGAGCACCCGATCGAAGTCCCAGTTGGTAAAGCAACACTGGGTCGTATCATGAACGTACTGGGTCAGCCAGTAGACATGAAGGGCGACATCGGTGAAGAAGAGCGTTGGGCT---------------ATCCACCGTGAAGCACCATCCTATGAAGAGCTGTCAAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTTGCGAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTTATTCGTAACATCGCGATCGAGCACTCCGGTTATTCTGTGTTTGCGGGCGTAGGTGAACGT [...]
+spp2 CTTGAGGTACAAAATGGTAATGAG------AGCCTGGTGCTGGAAGTTCAGCAGCAGCTCGGTGGTGGTATCGTACGTGCTATCGCCATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTTAAAGACCTTGAGCACCCGATCGAAGTCCCGGTTGGTAAAGCAACGCTGGGTCGTATCATGAACGTGCTGGGTCAGCCGATCGATATGAAAGGCGACATCGGCGAAGAAGAACGTTGGGCG---------------ATTCACCGTGCAGCACCTTCCTATGAAGAGCTCTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTCGCGAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTTGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAACACTCCGGTTACTCCGTGTTTGCTGGTGTTGGTGAGCGT [...]
+spp3 CTTGAGGTACAGAATAACAGCGAG------AAGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCAATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTGAAAGACCTCGAGCACCCGATCGAAGTCCCGGTAGGTAAAGCGACCCTGGGTCGTATCATGAACGTGCTGGGTCAGCCAATCGATATGAAAGGCGACATCGGCGAAGAAGATCGTTGGGCG---------------ATTCACCGCGCAGCACCTTCCTATGAAGAGCTGTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATTTGTCCGTTCGCTAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGCGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAGCACTCCGGTTACTCCGTGTTTGCAGGCGTGGGTGAGCGT [...]
+spp4 CTCGAGGTGAAAAATGGTGATGCT------CGTCTGGTGCTGGAAGTTCAGCAGCAGCTGGGTGGTGGCGTGGTTCGTACCATCGCCATGGGTACTTCTGACGGCCTGAAGCGCGGTCTGGAAGTTACCGACCTGAAAAAACCTATCCAGGTTCCGGTTGGTAAAGCAACCCTCGGCCGTATCATGAACGTATTGGGTGAGCCAATCGACATGAAAGGCGACCTGCAGAATGACGACGGCACTGTAGTAGAGGTTTCCTCTATTCACCGTGCAGCACCTTCGTATGAAGATCAGTCTAACTCGCAGGAACTGCTGGAAACCGGCATCAAGGTTATCGACCTGATGTGTCCGTTCGCTAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGGCTGAGCACTCAGGTTATTCGGTATTTGCTGGTGTGGGTGAGCGT [...]
diff --git a/tests/christof/greedy-raxml-protein/Als_etal_2004.phy b/tests/christof/greedy-raxml-protein/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/greedy-raxml-protein/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/greedy-raxml-protein/partition_finder.cfg b/tests/christof/greedy-raxml-protein/partition_finder.cfg
new file mode 100755
index 0000000..80fb2c8
--- /dev/null
+++ b/tests/christof/greedy-raxml-protein/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/model-greedy-phyml01/Als_etal_2004.phy b/tests/christof/model-greedy-phyml01/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/model-greedy-phyml01/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/model-greedy-phyml01/partition_finder.cfg b/tests/christof/model-greedy-phyml01/partition_finder.cfg
new file mode 100755
index 0000000..0841f49
--- /dev/null
+++ b/tests/christof/model-greedy-phyml01/partition_finder.cfg
@@ -0,0 +1,25 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = MtArt+I+G+F, WAG+I+G+I;
+
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/model-greedy-phyml02/Als_etal_2004.phy b/tests/christof/model-greedy-phyml02/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/model-greedy-phyml02/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/model-greedy-phyml02/partition_finder.cfg b/tests/christof/model-greedy-phyml02/partition_finder.cfg
new file mode 100755
index 0000000..9d8f29a
--- /dev/null
+++ b/tests/christof/model-greedy-phyml02/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = MtArt+I+G+F, WAG+I+G;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/model-greedy-phyml03/Als_etal_2004.phy b/tests/christof/model-greedy-phyml03/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/model-greedy-phyml03/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/model-greedy-phyml03/partition_finder.cfg b/tests/christof/model-greedy-phyml03/partition_finder.cfg
new file mode 100755
index 0000000..c04955b
--- /dev/null
+++ b/tests/christof/model-greedy-phyml03/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = MtArt+I+G+F, WAG+I+G, WAG+LG+F+I;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/model-greedy-raxml01/Als_etal_2004.phy b/tests/christof/model-greedy-raxml01/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/model-greedy-raxml01/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/model-greedy-raxml01/partition_finder.cfg b/tests/christof/model-greedy-raxml01/partition_finder.cfg
new file mode 100755
index 0000000..f929aaf
--- /dev/null
+++ b/tests/christof/model-greedy-raxml01/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = WAG+F, LG+I+F;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/model-greedy-raxml02/Als_etal_2004.phy b/tests/christof/model-greedy-raxml02/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/model-greedy-raxml02/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/model-greedy-raxml02/partition_finder.cfg b/tests/christof/model-greedy-raxml02/partition_finder.cfg
new file mode 100755
index 0000000..5ea2351
--- /dev/null
+++ b/tests/christof/model-greedy-raxml02/partition_finder.cfg
@@ -0,0 +1,25 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = MtArt+I+G+F WAG+I+G;
+
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/model-greedy-raxml03/Als_etal_2004.phy b/tests/christof/model-greedy-raxml03/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/model-greedy-raxml03/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/model-greedy-raxml03/partition_finder.cfg b/tests/christof/model-greedy-raxml03/partition_finder.cfg
new file mode 100755
index 0000000..5c07cdf
--- /dev/null
+++ b/tests/christof/model-greedy-raxml03/partition_finder.cfg
@@ -0,0 +1,25 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = MtArt+I+G+F, WAG+I+G;
+
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/overlap-error/Als_etal_2004.phy b/tests/christof/overlap-error/Als_etal_2004.phy
new file mode 100755
index 0000000..76d61e5
--- /dev/null
+++ b/tests/christof/overlap-error/Als_etal_2004.phy
@@ -0,0 +1,5 @@
+ 4 949
+AD00P055 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXX [...]
+RV03N585 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYITSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXIILIF [...]
+TDA99Q996 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXXIISXIISQESXKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLXIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMXXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/christof/overlap-error/partition_finder.cfg b/tests/christof/overlap-error/partition_finder.cfg
new file mode 100755
index 0000000..48854b3
--- /dev/null
+++ b/tests/christof/overlap-error/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Als_etal_2004.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = all;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+COI = 1-407;
+COII = 408-624;
+EF1a = 625-949 1 3;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/christof/test_christof.py b/tests/christof/test_christof.py
new file mode 100644
index 0000000..ce51dff
--- /dev/null
+++ b/tests/christof/test_christof.py
@@ -0,0 +1,86 @@
+"""Incorporate some tests from Christoph Mayer (originally in Perl)"""
+# TODO This could be automated in the same way "full_analysis'
+
+import os
+import inspect
+import pytest
+from partfinder import main, util, analysis, config, alignment
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+# Far too clever function
+def path_from_function():
+ funname = inspect.stack()[1][3]
+ # remove test_
+ funname = funname[5:]
+ funname = funname.replace('_', '-')
+ pth = os.path.join(HERE, funname)
+ return pth
+
+# ---------------- SUCCESS ---------------------
+
+def test_greedy_phyml_dna():
+ main.call_main("DNA", '"%s"' % path_from_function())
+
+def test_greedy_raxml_dna():
+ main.call_main("DNA", '"%s" --raxml' % path_from_function())
+
+def test_greedy_phyml_protein():
+ main.call_main("protein", '"%s"' % path_from_function())
+
+def test_greedy_raxml_protein():
+ main.call_main("protein", '"%s" --raxml' % path_from_function())
+
+def test_clustering_raxml_dna():
+ main.call_main("DNA", '"%s" --raxml' % path_from_function())
+
+
+# ---------------- ERRORS ---------------------
+# Check the exception, and then look in the log output for specific
+# details of the exception.
+
+def test_alignment_error(caplog):
+ with pytest.raises(alignment.AlignmentError):
+ main.call_main("protein", '"%s"' % path_from_function())
+ assert "Site 1000 is specified in [data_blocks], but the alignment only has 949 sites." in caplog.text()
+
+def test_overlap_error(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("protein", '"%s"' % path_from_function())
+ assert "sites overlap in your block definitions" in caplog.text()
+
+def test_clustering_phyml_dna(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s"' % path_from_function())
+ assert "Clustering methods are only available when using raxml" in caplog.text()
+
+def test_model_greedy_phyml01(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s"' % path_from_function())
+ assert "'WAG+I+G+I' is not a model/list that is implemented in PartitionFinder. Perhaps you made a mistake." in caplog.text()
+
+def test_model_greedy_phyml02(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s"' % path_from_function())
+ assert "'MTART+I+G+F, WAG+I+G' is/are not a valid model(s) or lists" in caplog.text()
+
+def test_model_greedy_phyml03(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s"' % path_from_function())
+ assert "'WAG+LG+F+I' is not a model/list that is implemented in PartitionFinder." in caplog.text()
+
+def test_model_greedy_raxml01(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s" --raxml' % path_from_function())
+ assert "'LG+I+F, WAG+F' is/are not a valid model(s) or lists of models" in caplog.text()
+
+def test_model_greedy_raxml02(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s" --raxml' % path_from_function())
+ assert "Expected ";" (at char 284), (line:9, col:22)" in caplog.text()
+
+def test_model_greedy_raxml03(caplog):
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s" --raxml' % path_from_function())
+ assert "'MTART+I+G+F, WAG+I+G' is/are not a valid model(s)" in caplog.text()
+
diff --git a/tests/clustering/DNA_hcluster1/Caterino_2001.phy b/tests/clustering/DNA_hcluster1/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster1/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster1/cmdline.txt b/tests/clustering/DNA_hcluster1/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/DNA_hcluster1/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster1/partition_finder.cfg b/tests/clustering/DNA_hcluster1/partition_finder.cfg
new file mode 100644
index 0000000..c40b231
--- /dev/null
+++ b/tests/clustering/DNA_hcluster1/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster1/results.bin b/tests/clustering/DNA_hcluster1/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_hcluster1/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster2/Caterino_2001.phy b/tests/clustering/DNA_hcluster2/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster2/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster2/cmdline.txt b/tests/clustering/DNA_hcluster2/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/DNA_hcluster2/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster2/partition_finder.cfg b/tests/clustering/DNA_hcluster2/partition_finder.cfg
new file mode 100644
index 0000000..8d239c8
--- /dev/null
+++ b/tests/clustering/DNA_hcluster2/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+I+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster2/results.bin b/tests/clustering/DNA_hcluster2/results.bin
new file mode 100644
index 0000000..45ddc80
--- /dev/null
+++ b/tests/clustering/DNA_hcluster2/results.bin
@@ -0,0 +1 @@
+�]q(G��
D1z�NG@�tD1z�NG@�w����hG@�L��?�e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster3/Caterino_2001.phy b/tests/clustering/DNA_hcluster3/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster3/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster3/cmdline.txt b/tests/clustering/DNA_hcluster3/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/DNA_hcluster3/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster3/partition_finder.cfg b/tests/clustering/DNA_hcluster3/partition_finder.cfg
new file mode 100644
index 0000000..c07f165
--- /dev/null
+++ b/tests/clustering/DNA_hcluster3/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC;
+model_selection = aic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster3/results.bin b/tests/clustering/DNA_hcluster3/results.bin
new file mode 100644
index 0000000..b5ddbd9
Binary files /dev/null and b/tests/clustering/DNA_hcluster3/results.bin differ
diff --git a/tests/clustering/DNA_hcluster4/Caterino_2001.phy b/tests/clustering/DNA_hcluster4/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster4/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster4/cmdline.txt b/tests/clustering/DNA_hcluster4/cmdline.txt
new file mode 100644
index 0000000..de6e319
--- /dev/null
+++ b/tests/clustering/DNA_hcluster4/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "1, 1, 1, 1"
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster4/partition_finder.cfg b/tests/clustering/DNA_hcluster4/partition_finder.cfg
new file mode 100644
index 0000000..e9e7067
--- /dev/null
+++ b/tests/clustering/DNA_hcluster4/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster4/results.bin b/tests/clustering/DNA_hcluster4/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_hcluster4/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster5/Caterino_2001.phy b/tests/clustering/DNA_hcluster5/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster5/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster5/cmdline.txt b/tests/clustering/DNA_hcluster5/cmdline.txt
new file mode 100644
index 0000000..7ea31ef
--- /dev/null
+++ b/tests/clustering/DNA_hcluster5/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "0,0,0,0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster5/partition_finder.cfg b/tests/clustering/DNA_hcluster5/partition_finder.cfg
new file mode 100644
index 0000000..e9e7067
--- /dev/null
+++ b/tests/clustering/DNA_hcluster5/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster5/results.bin b/tests/clustering/DNA_hcluster5/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_hcluster5/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster6/Caterino_2001.phy b/tests/clustering/DNA_hcluster6/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster6/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster6/cmdline.txt b/tests/clustering/DNA_hcluster6/cmdline.txt
new file mode 100644
index 0000000..11f888e
--- /dev/null
+++ b/tests/clustering/DNA_hcluster6/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "1000, 0.01, 0.003, 0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster6/partition_finder.cfg b/tests/clustering/DNA_hcluster6/partition_finder.cfg
new file mode 100644
index 0000000..e9e7067
--- /dev/null
+++ b/tests/clustering/DNA_hcluster6/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster6/results.bin b/tests/clustering/DNA_hcluster6/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_hcluster6/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster7/Caterino_2001.phy b/tests/clustering/DNA_hcluster7/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_hcluster7/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_hcluster7/cmdline.txt b/tests/clustering/DNA_hcluster7/cmdline.txt
new file mode 100644
index 0000000..0339783
--- /dev/null
+++ b/tests/clustering/DNA_hcluster7/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "-1000, 0.01, 0.003, 0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_hcluster7/partition_finder.cfg b/tests/clustering/DNA_hcluster7/partition_finder.cfg
new file mode 100644
index 0000000..e9e7067
--- /dev/null
+++ b/tests/clustering/DNA_hcluster7/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = hcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_hcluster7/results.bin b/tests/clustering/DNA_hcluster7/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_hcluster7/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster1/Caterino_2001.phy b/tests/clustering/DNA_rcluster1/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster1/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster1/cmdline.txt b/tests/clustering/DNA_rcluster1/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/DNA_rcluster1/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster1/partition_finder.cfg b/tests/clustering/DNA_rcluster1/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster1/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster1/results.bin b/tests/clustering/DNA_rcluster1/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster1/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster10/Caterino_2001.phy b/tests/clustering/DNA_rcluster10/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster10/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster10/cmdline.txt b/tests/clustering/DNA_rcluster10/cmdline.txt
new file mode 100644
index 0000000..cfd74e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster10/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent "99.999999"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster10/partition_finder.cfg b/tests/clustering/DNA_rcluster10/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster10/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster10/results.bin b/tests/clustering/DNA_rcluster10/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster10/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster11/Caterino_2001.phy b/tests/clustering/DNA_rcluster11/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster11/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster11/cmdline.txt b/tests/clustering/DNA_rcluster11/cmdline.txt
new file mode 100644
index 0000000..4d5675c
--- /dev/null
+++ b/tests/clustering/DNA_rcluster11/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent "100.00"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster11/partition_finder.cfg b/tests/clustering/DNA_rcluster11/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster11/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster11/results.bin b/tests/clustering/DNA_rcluster11/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster11/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster12/Caterino_2001.phy b/tests/clustering/DNA_rcluster12/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster12/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster12/cmdline.txt b/tests/clustering/DNA_rcluster12/cmdline.txt
new file mode 100644
index 0000000..fe8a560
--- /dev/null
+++ b/tests/clustering/DNA_rcluster12/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent "100.001"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster12/partition_finder.cfg b/tests/clustering/DNA_rcluster12/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster12/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster12/results.bin b/tests/clustering/DNA_rcluster12/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster12/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster13/Caterino_2001.phy b/tests/clustering/DNA_rcluster13/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster13/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster13/cmdline.txt b/tests/clustering/DNA_rcluster13/cmdline.txt
new file mode 100644
index 0000000..e8b7f22
--- /dev/null
+++ b/tests/clustering/DNA_rcluster13/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent "-0.001"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster13/partition_finder.cfg b/tests/clustering/DNA_rcluster13/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster13/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster13/results.bin b/tests/clustering/DNA_rcluster13/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster13/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster14/alignment.phy b/tests/clustering/DNA_rcluster14/alignment.phy
new file mode 100644
index 0000000..faa8d95
--- /dev/null
+++ b/tests/clustering/DNA_rcluster14/alignment.phy
@@ -0,0 +1,66 @@
+65 4027
+Maurolicus TAAGAGGTCCCGCCTGCCCAGTGAC-CA-T-GT-GTTCAACGGCCGCGGTATTTTAACCGTGCAAAGGTAGCGCAATCACTTGTCTCTTAAATAGAGACCTGTATGAATGGCACAACGAGGGCTCACCTGTCT-CCTCCTCCC-AGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAACACCCCCATAAGACGAGAAGACCCCATGGAACTTTAGA-CAC--T--AG-A-C-AA-CG-C-ACT-T-TTC-AT-T--C--CC----T--C-CT--T-TCT--C-GA-G-CG----AC-C---AC-GTGC--C-G--C-CCTG-TC-TCCTTGTCTTTGGTTGGGGTGACCCCGGAGA-ATAATGA-AACCT-CC-CCA-AGA-AA-C-AAG-A--G-C--A-C------CA-C-TCTCACA-A-CTA-AG-G-CCAACAACCCCAAGTA-CCAGA-ACCTCTGA-T [...]
+Lota TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAATTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AG-G-TAAGTCA-C-G-T---TTA-A--T--AT-AC-T-AGA-A-TA----ACA--G-TA-A-AA-A---C-TT--AG--T-G--A-T--A-TTTATC--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAT-A-CTC-AGAG-CC-TCTACTCCAAGTA-ACAGA-AATTCTGACT [...]
+Gadus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCATCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAATTACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--AA-G-TAAGTCA-C-G-T---TTA-A--C--AT-GC-T-GTG-A-TA----ACA--G-TA-A-AA-A---C-TT--AG--T-G--A-T--A-TTTACT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAT-A-CTC-AGAG-CC-TCTACTCCAAGTA-ACAGA-AATTCTGACT [...]
+Gaidropsarus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCCCTCC-AATCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAGTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAATTCA-C-GTT---TTA-A--T--AC-CC-T-GTT-A-TA----CCA--G-TA-A-AA-A---C-TT--AG--T-T--T-T--A-CTTATT--GAAGTGTCTTTGGTTGGGGCGACCACGGGGA-AAAATAT-AACCC-CC-ATG-AAG-AC---CGG-GG-A-T--A-C-T--A-T--C-CCT-AAT-A-CTC-AGAGCTT-TCTACTCCAAGTA-ACAGA-AATTCTGACT [...]
+Zu TAAGAGGCCACGCCTGCCCGGTGAC-TA-G-AA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAAAGGCGAGACGAGGGCAAAACTGTCT-CCCTTCTCA-TGTCAATGAAACTGATTTCCCCGTGCAGAAGCGGGGATGCAGTCACAAGACGAGAAGACCCTGTGGAGCTTTAGA--C-T-T--TA-G---TG--A-G-C-TTGCC-C-A--A--A--GT-A--T--A-AACCCCAAC--T-AT-ATAA-A--AA-CA--C---G-GC-T-A--C-CCTC-CCCTAAATGTCTTTGGTTGGGGCGACCGCGGAGATAA-AC-TAAACCA-CC-GCG-TGG-A--TAGGG-G--G-T-TA-A----C-C----CCT-ATA-A-TTA-AGAG-CT-ACAGCTCTATATA-TCAGG-ATTCCTGA-C [...]
+Trachipterus TAGGAGGCCACGCCTGCCCGGTGAC-TA-A-AA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCGAAACGAGGGCGAAACTGTCT-CCCCCCTTA-GGTCAATGAAACTGATCTCCCCGTGCAGAAGCGGGGATAGACCCACAAGACGAGAAGACCCTATGGAGCTTGAGA--C-T-T--TA-A---GG--A-G-C-CTGCC-C-T--A--A--GC-T--T--T-AACTT-AAT--T-GA-A-TG-A--AC-CC--C---G-GC-T-T--C-CCTC-CCCCAAATGTCTTTGGTTGGGGCGACTGCGGAGATAATAC-T-AACCC-CC-GCG-TGG-A--T-TGG-G--G----A-C----T-C----CCT-ATA-A-TCT-AGAG-CT-ACGGCTCTAAATA-TCAGA-ATTTCTGA-C [...]
+Regalecus TAAGAGGCCCCGCCTGCCCGGTGAC--G-A-AA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAAAGGCGACACGAGGGCAAATCTGTCT-CCCCCCTCC-AGTCAATGAAACTGATCTCCCCGTGCAGAAGCGGGGATACAACCACAAGACGAGAAGACCCTGTGGAGCTTCAGA--C-T-T--TG-G---TA--A-G-C-CTGCCTC-A--A-CC--CC-T--C--T-GA--C-AAA--G-GA-G-GGTT--AA-CA--C---A-GCAT-C--C-CCTT-ATTTAAATGTCTTTGGTTGGGGCGACCACGGAGATAATTT-T-AACCC-CC-GCG-GGG-A----TAG-G--G----A-C-T--T-T----CCT-ATA-A-CCC-AGAG-CT-ACAGCTCTAAGTG-TCAAG-ACTCTTGA-C [...]
+Lophotus TAGGAGG-CCCGCCTGCCCGGTGAC-TA-T-TA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCCTTTAAATAGGGACTAGTATGAATGGCGAAACGAGGGTGTAACTGTCT-CCCCCATCC-GGTCAATGAAACTGATCTCCCCGTGCAGAAGCGGGGATGAACACACAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-C--TG-G---AGT-A-T-A-C-CCCTT-T--T--C--CC-T--C--A-TA--T-AAA--G-TT-T-GG-A--AA-CTC-TG--G-GTGT-A--C-CCTC-CCAAGACTGTCTTTGGTTGGGGCGACCGCGGAGAGAACAC-T-ACCCC-CC-GCG-TGG-A--TGAAGTG--A----A-C-A--A-C----TTT-TTA-A-CCT-AGAG-CT-ACACCTCTAAGTG-TCAGA-ATATATGG-C [...]
+Ijimaia TAAGAGGTCCCGCCTGCCCTGTGAC-AA-T-TA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATTACGAGGGCTTAGCTGTCT-CCTTGCCCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACACCATAAGACGAGAAGACCCTGTGGAGCTTTAAATTA---T--AA-G-T-AG-AC-T-G-T-G-TTA-AT-A--CG-CC----A--A-AA--T-AAA-GG-AA-A-CT-AA-AC-CA--AA--TAG----A--C-ACTA-CT-TTAATATTTTTGGTTGGGGCGACCACGGGGG-ACAAATA-AGCCC-CC-ACG-AGG-AC-C-AGG-A----A--A-A----T-CT-T-CCT-AAA-A-CCA-AGAG-CT-ACAGCTCTAAGAA-ACAGA-ACTTCTGA-C [...]
+Coccorella TAAGAGGTCCTGCCTGCCCGGTGACTCA-A-AAAGTTAAACGGCCGCAGTATCTTAACTGTGCGAAGGTAGCGCAATCACTTGTCCTTTAATTGAGGACCTGTATGAATGGCAAGACGAGGGCTTAGCTGTCT-CCCCTGCCC-CGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGTTAACCCTATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA---ACCAA-A-C-GC-CT-C-A-C---ATA-A--GACAG-CC-T--A--A-AA--G-AAA--A-AA-GCTG--C-CC-ATCTTA-GTGA--C-A--C-CCT-CCGGTTTATGTCTTTGGTTGGGGCGACCGTGGGGA-AAAGAAA-ACCCC-CC-ATG-AAG-ACGTTAAA-G--A-C--T-C---T---C-T-TTT-ATA-A-CCA-AGAGCCT-ACTACTCAAAGTA-TCAGACACCTCTGA-C [...]
+Lampris TAAGAGGTCCCGCCTGCCCCGTGAC-AA-T-A--GTTTAACGGCCGCGGTATTCTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCACCACGAGGACTTAGCTGTCT-CCCCTCTCC-CGTCAGTAAAATTGACCTACCCGTGCAGAGGCGGGTACACCCCCACAAGACGAGAAGACCCTGTGGAGCTTTAGG-CC-CAA--GA-A---AG--AGG-A---C-ATC-A--A--G---C----C------------A----GA-A-AC-A--GC-CA--CA--G-CC-T-A--T-CTT--TC-CCAATGCCTTTGGTTGGGGCGACCACGGAGATAAAAC-A-AACCC-CC-GCG-TGG-AC-C-GAG-A--G----A-C-C--T-C--T-CTT-AGA-A-CTA-AGAG-CC-ACCCCTCCAAGCA-CCAGA-ACATCTGA-C [...]
+Velifer TAAGAGGCACCGCCTGCCCTGTGAC-TT-T-AT-GTTTAACGGCCGCGGTATCCTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCTCTCT-AGTCAGTAAAACTGATCTCCCCGTGCAGAAGCGGGGTTGCCCACACAAGACGAGAAGACCCTGTGGAGCTTTAGA-TA-T-A--AA-G---AG--GGGCACCT-TAAG-A--A--G-TCC----C--G-TA----AAA--G-GA-ACCCAA--TC-CC--CA--GTGC-A-C--T-CCT--TCTCGAATATCTTTGGTTGGGGCGACCGCGGGGA-CAAAC-AGAACCC-CC-ACG-AGG-AC-T-AAG-A--G-T--A-C-C--C-C--T-CCT-AAA-A-CCA-AGAG-CC-ACCACTCTAAGTA-CTAGA-ACATCTAA-C [...]
+Benthosema TAAGAGGTCCCGCCTGCCCAGTGACTAA-T-ATAGTTAAATGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACTGGTATGAACGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTAA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATATACTCGTAAGACGAGAAGACCCTATGGAGCTTAAGA-TA-TAA--AGTT-C-AA-CC-C-A-C-G-TCA-A--A--CA-CC-T-------CC--T-AAA--A-G--A-AT-A--AA-CA--AA-AT-G--A-A--C-CTTG-CT-GATATATCTTCGGTTGGGGCGACCACGGGGA-AAGACAA-AACCC-CC-ACA-TGG-AC-C-GGG-G--C-A--CCC----A-CA-C-CCT-AGA-A-CAT-AGAC-CC-ACAGGTCAAATCA-ACAGC-ACTTCTGA-C [...]
+Neoscopelus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAAAGGCACCACGAGGGCTTAACTGTCT-CCCCTTTAG-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACCCCGTAAGACGAGAAGACCCTATGGAGCTTAAGA-CA-C-A--AA-G-C-GG-CC-C-A-C-G-TCA-A--G--TA-CC----C--C-GAT-T-CAA--G-GC-A-AT-A--AA-CA--AA-GT-GC-T-A--CGCCCG-CC-GAAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAGAAAA-AACCC-CC-ACG-TGG-AC-C-GGG-G--C-T--A-C----A-CA-C-CCT-AGA-A-CCA-AGAC-CC-ACAGATCAAAGCA-ACAGA-ACTTCTGA-C [...]
+Triacanthodes TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCACGACGAGGGCTTAGCTGTCT-CCTCATTC-AAGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAACCATAAGACGAGAAGACCCTATGGAGCTTTAGA-CACC-A--GA-G-T-AG-AT-C-A-T-G-TTA-AACA--AC-CC-T-TAATT-AA----A-G----GA-CTA--A--AC-CA-AAT--G-C--C-T--A-CT-A-CC-CCCATGTCTTTGGTTGGGGCGACCGCGGGGA-AACACAA-AACCC-CC-GTG-TGG-AA-C-GGG-A--A-C--A-C--CCC-C--T-CCT-ACA-G-CTA-AGAG-TC-TCCACTCTAACGC-ACAGA-ATATCTGA-C [...]
+Gasterosteus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTATTACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CACT-A--AA-G-T-GG-AT-C-A-T-G-TCA-AT-G--AC-CC-T-AAA-T-AA----A-G----GA-TTG--A--AC-AA-GAT--G-G--A-A--C-CC-A-CC-CTGATGTCTTTGGTTGGGGCGACCGCGGGGA-AATAAAT-AACCC-CC-ATG-TGG-AA-T-GGG-A--G-C--A-C--C-C-C--T-CCT-ACA-G-CTG-AGAG-TT-ACAACTCTAATAA-ACAGA-ATTTCTGA-C [...]
+Morone TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATCTTAACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATAACGAGGGCTTAACTGTCT-CCTTTCTC-AAGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTAACACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA-T-A--AG-A-T-AG-AT-T-A-C-C-TTA-ATCA--AC-CC-A-GAA-C-AA----A-G----GG-CGG--A--AC-CA-GAG--G-T--A-A--A-CC-T-TT-CCAACGTCTTTGGTTGGGGCGACCGTGGGGT-AAAACAA-AACCC-CC-ATG-TGG-AA-T-AGG-A--G-C--A-C--C-T-C--T-CCT-TCA-A-CCT-AGAG-CT-CCCGCTCTAAGGA-ACAGA-ATTTCTGA-C [...]
+Capros TAAGAGGTCCCGCCTGCCCTGTGAC-TG-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCTTTTTC-AAGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATACTTACATAAGACGAGAAGACCCTATGAAGCTTTAGA-CACC-A--AA-G-C-AG-CT-C-A-A-G-TTA-AACA--CC-CC-C-TCA-T-AA----G-G----GA-CTA--A--AC-CA-TGT--G-A--A-T--C-CT-G-CC-CTAATGTCTTTGGTTGGGGCGACCGCGGGG--GATAAAA-AGCCC-CC-ATG-TGG-AA-T-GAG-A--T-T--A----ATT-C--T-CTT-AAA-A-CTA-AGAG--CTACCGCTCTAAGAA-ACAGA-ACTTCTGA-C [...]
+Beryx TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CTTTTCTCCAAGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATACAAACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA-C-A--AA-G-C-AG-CC-C-A---A-ATT-A--A--GA-CT-C--CA-A-AA-TTAAAACGG-AG-C----A--AT-AA--AA--T-G--A-CAAC-CCTG-CT-CAAATGTCTTTGGTTGGGGCGACCATGGGGA-AAAACGA-AACCC-CC-ACG-TGG-AA-C-GGA-A--G-A--A-C----TTC--T-TCT-ACA-A-CCA-AGAG-CC-GCCACTCCAAGTG-ACAGA-ATCTCTGA-C [...]
+Melamphaes TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTCAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCCTGACGAGGGCTTAGCTGTCT-CTTTTCTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTTTCTCATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA-C-A--AA-G-C-AA-CC-C-A---A-ATT-A--C--GA-CC-T--TG-A-AA-CTAAACCAG-GG-C----A--AT-AA--AA--T-G--A-C--C-CCTG-CT-CAACTGTCTTTGGTTGGGGCGACCCTGGGGA-AAAACAA-AACCC-CC-ACG-TGG-AA-C-AGA-A--G-A--A-C----CCC--T-TCT-ACA-A-CCA-AGAG-CC-CCTGCTCTAAGTA-ACAGA-ACCTCTGA-C [...]
+Rondeletia TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACAACGAGGGCTTAGCTGTCT-CCTTTTTCT-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTATAACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CA-C-A--AA-G-C-AG-TC-C-A-C-A-CCA-A--A--CA-CC-C--CA-A-AA--T-AAA-GG-GG-C-A--A--AT-CA--AG--TGG--T-C--C-CCTG-CT-CAAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAAATAA-AACCC-CC-ACG-TGG-AA-T-GAG-A--G-A--A-C----CTC--T-CCC-ACA-A-CCA-AGAG-CC-GCCACTCTAAGTA-ACAGA-ACCTCTGA-C [...]
+Sargocentron TAAGAGGTCCCGCCTGCCCCGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCCTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTAATCTCCCCGTGCAGAAGCGGGGATAAAACCATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CA---A--AA-GAC-GG-AC-C-T-T-G-CAA-A--A--CA-AC-C--CT-G-AA--C-AAA--G-GA-C-A--A--AA-CACCAA--AGG--A-C--T-CC-G-CC-CAAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAAATAA-AACCC-CC-ACG-TGG-AA-T-GGG-A--G-A--A-C----ATC--C-CCC-AAA-A-CTA-AGAG-GT-ACCCCTCTAAGAA-GCAGA-ATATCTGA-C [...]
+Xenolepidichthys TAAGAGGTCCCGCCTGCCCTGTGAC--T-T-TA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCG-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATGCAAATATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--GT-G-C-AG-AT-C-A-C---GAA-A--A--AT-ACTT--T--A-TA-----CA--AAAAGATTA-A--GC-CC--AA--T-G--A-C--T-CCCGCA--TGACTGTCTTTGGTTGGGGCGACCACGGGGA-AAAATAA-AACCC-CC-ACG-AGG-AC-TGAG--AGTT-T------T--A-C--T-CCT-AAA-A-CCA-AGAG-CT-ACAGCTCTAAGTA-TCAGA-AATTCTGA-C [...]
+Allocyttus TAAGAGGTCCCGCCTGCCCTGTGAC--T-T-WA-GTTTAACGGCCGCGGTATYTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAATAACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CC-T-A--GT-G-C-AG-AT-C-A-C---GAA-A--A--AT-ACTT--TA-A-GA----CAA--AAAAGA-AA-A--GC-CC--AA--T-G--A-C--C-CCTGCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ACG-AGG-AC-TGAG--AGTT-T------T--A-C--T-CCT-AAA-A-CCA-AGAG-CC-ACAGCTCTAAGTA-TCAGA-AATTCTGA-C [...]
+Zenopsis TAAGAGGTCCCGCCTGCCCTGTGAC--T-TAAA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATGATAATATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--GT-G-A-AG-AC-C-A-C---GAA-A--A--AA-GCTT--TG-AGTT-----AA--AAAAGA-AA-A--CC-CC--AG--T-G--A-T--T-TCTCCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ACG-AGG-AT-TGAG--AGTT-C------A--A-C--T-CCT-AAA-A-CCA-AGAG-CT-ACAGCTCTAAGAA-ACAGA-AATTCTGA-C [...]
+Zeus TAAGAGGTCCCGCCTGCCCTGTGAC--T-TAAA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAATAATATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--AT-G-C-AG-TC-C-A-C---GAATA--A--TA-CTTT--TG-A-TG-----AA--GAAAGA-AA-A--GC-TC--AA--T-G--G-C--T-CCTGCA--CGCCTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ATG-AGG-AT-TGAG--AGTT-C------T--A-C--T-CCT-AAA-A-CCA-AGAG-CC-ACAGCTCTAAGTA-ACAGA-AATTCTGA-C [...]
+Zenion TAAGAGGTCCCGCCTGCCCTGTGAC-TT-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCT-AGTCAATGAAATTGATATCCCCGTGCAGAAGCGGGGATATTCACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--GT-G-C-AG-CC-C-A-C---GAA-A--A--AT-ACTT--TT-A-CA----CAA--GAAAGA-AA-A--GC-CC--AA--T-G--G-C--C-CCCGCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGAA-AAAACAA-AACCC-CC-ACG-AGG-AG-T-GGA-AGCA-C--A---A--G-C--C-ACC-CAA-G-CCA-AGAG-CC-ACAGCTCTAAGCA-TCAGA-AATTCTGA-C [...]
+Parazen TAAGAGGTCCCGCCTGCCCTGTGAC-TT-T-AA-GTTTAACGGCCGCGGTATCTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--GT-G-C-AG-CC-C-A-C----AA-A--A--AT-GCTT--TA-A-AA----CAA--AAAA-C-AA-A---C-CC--AA--C-G--A-G--C-CCTGCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ACG-AGG-AC-T-AGA-AGTT-T--A---T--A-C--T-CCT-ATA-A-CCA-AGAG-CC-ACGGCTCTAAGTC-TCAGA-AATTCTGA-C [...]
+Cyttopsis TAAGAGGTCCAGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGAATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAGGACCCGTATGAATGGCTCCACGAGGGCTTAACTGTCT-CCTTTTTCA-GGTCGATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAATTACATAAGACGAGAAGACCCTGTGGAGCTTAAGA-CC-C-A--AT-G-C-AG-GA-C-ACC---TAC-T--A--AC-AC-T--TT-A-GA----CAA--TAAAGACTG-A--GA-CA--TA--T-G--A-C--C-CCTGCA--AGACGGTCTTTGGTTGGGGTGACCGAGGGGA-AAAACAA-AGCCC-CC-ACG-AGG-AC-T-AGG-AG-T-C--T---T--A-C--T--CT-AAA-A-CCA-AGAG-CC-ACAACTCTAAGTA-TCAGA-AATTCTGA-C [...]
+Hoplostethus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACGACGAGGGCCTAGCTGTCT-CCTTTTTCA-GGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATAATCACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CA-C-A--AG-G-C-AG-CC-C-A-C-G-TTA-A--T--AA-CT-T--TC-A-AA--C-AAG--A-AA-CAA--A--AC-TA--AG--TGG--C-G--C-CCTG-CC-AGAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ATG-TGGAAA-A-GGA-G--G-AC-A------C-C--T-CCT-ACA-A-CCC-AGAG-CC-ACTGCTCGAAGTA-ACAGA-ACTTCTGA-C [...]
+Diretmus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-A-TT-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCCGTATGAACGGCACGACGAAGGCCCAGCTGTCT-CCTTTTTCA-GGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATGTTAACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CC-C-A--AG-G-C-AG-CC-C-A-C-G-TCA-A--G--CA-CC-C--CC-C-GA--C-AAA--G-GG-TTA--A--AC-CA--AG--TGA--A-G--C-TCTG-CC-CCAGTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACTA-AACCC-CC-ATG-TAGATA-A-GGA-A--T-A--G-C----C-C--T-CCT-ACA-A-CCA-AGAG-TC-ACCACTCTAAGCA-ACAGA-AATTCTGA-C [...]
+Polymixia_japonica TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCTTAACTGTCT-CCCCTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTGAAA-CC-T----AT-GAT-AG-TA-C-A-C-G-TCA-A--A--CA-CC-T--CA-A-CA--T-AAA--G-AA-A-AG-A--AC-TA--AG--T-G--T-C-TC-CCTA-TC-AAAGTGTTTTTGGTTGGGGCGACCGC-GGGG-AAAACAA-AACCC-CC-ATG-TGG-AC-C-GGG-A--A-T--A-C-TA-A-T--T-CCT-ACA-A-CCCTAGAG-CT-ACCGCTCTAAGTA-ACAGA-ATATCTGA-C [...]
+Polymixia_lowei TAAGAGGTCCCGCCTGCCCTGTGAC-TC-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCTTAACTGTCT-CCCCTTTCT-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTGAAA-CC-T----AT-GAT-AG-TG-C-A-C-G-TCA-A--A--CA-CC-T--CA-G-CA--C-AAA--G-AA-A-AG-A--AC-TA--AG--T-G--T-T-TA-CCTA-TC-AAAGTGTTTTTGGTTGGGGCGACCGC-GGGG-AAAACAA-AACCC-CC-ATG-TGG-AC-C-GGG-A--A-T--A-C-TA-A-T--T-CCT-ACA-A-CCCTAGAG-CT-ACCGCTCTAAGTA-ACAGA-ACATCTGA-C [...]
+Percopsis_omiscomaycus TAAGAGGTCCCGCCTGCCCTGTGAC--A-A-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAACACATAAGACGAGAAGACCCTATGGAGCTTAAGA-CC-A-A--CC-T-C-GG-CC-C-A-T-G-TGG-A--G--C--AC-T--CA-A-C-----AAA--G-G--C-AG-A--AC-TA--AG--TGG--A----C-CCGA-G--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGG-ATCAACA-AGCCC-CC-ATG-TGG-AA-T-A-G-AG-A-A--A-CAT----C--T--CT-AGA-A-CCT-AGAG-CT-ACTGCTCCAAGTA-ACAGA-ACATCTGA-C [...]
+Percopsis_transmontana TGAGAGGTCCCGCCTGCCCTGTGAC--A-A-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAAAGGCATCACGAGGGCTTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATGCGCACATAAGACGAGAAGACCCTATGGAGCTTAAGA-CC-T-C--CC-C-C-GA-CC-C-A-T-G-TGA-C--A--C--AC-T--CA-A-C-----AAA--G-G--C-AG-A--AC-TT--AA--TGG--A-C--C-CCGG-G--AAACTGTCTTTGGTTGGGGCGACCGCGGGGG-ATGA-AA-AGCCC-CC-ATG-TGG-AA-T-A-G-AG-A-A--A-CAT----C--T--CT-AAA-A-CCC-AGAG-CC-ACTACTCCAAGTA-ACAGA-ACATCTGA-C [...]
+Forbesichthys TAAGAGGTCCCGCCTGCCCTGTGAC--A-T-CTAGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCATAACTGTCT-CCTCTCTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATATAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--CTC-C--CCTC-T-AA-CT-T-G-T-G-CAA-A--AG-CT-CC-T--CA-A-CA----ACA--G-GA-C-CA-A--AC-T---AA--T-A--A-G--C-CATA-G--AGACTGTCTTTGGTTGGGGCGACCTTGGGGA-ATAA-AA-AACCC-CC-ATG-CGG-AA-T-A-G--G-AGT--A-C-C----C--T-CCT-TAA-A-CCC-AGAG-CC-ACCCCTCGAAGTA-ACAAA-ACATTTGA-C [...]
+Speoplatyrhinus TAAGAGGTCCCGCCTGCCCTGTGAC--A-C-CTGGTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCTTAACTGTCT-CCTTTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGAGGATATAAACATAAGACGAGAAGACCCTGTGGAGCTTAAGA--C-T-C--CCTC-T-AA-CT-T-A-T-G-CAA-A--A--CT-CC-T--CA-A-TA----ACA--G-GA-C-CA-A--GC-T---AA--T-A--A-G--C-CACA-G--AAGCTGTCTTTGGTTGGGGCGACCCCGGGGA-ATAA-AA-AGCCC-CC-GTG-CGG-AA-T-A-A--G-AGT--A-T-T----C--T-CTT-TAA-A-CCC-AGAA-CC-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Amblyopsis TAAGAGGTCCCGCCTGCCCTGTGAC--A-C-CTAGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCTTAGCTGTCT-CCTCTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATATAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--C-C-C--CCTC-T-AA-CT-T-A-T-G-CAAGA--AG-CC-CC-T--CA-A-CA----ACA--G-GA-C-CA-A--GC-T---AA--T-A--A-G--G-CATA-G--AGCCTGTCTTTGGTTGGGGCGACCCTGGGGA-ATAA-AA-AACCC-CC-ATG-CGG-AA-C-A-G--G-ACT--C-C-C----C--T-CCT-TAA-A-CCC-AGAG-CG-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Typhlichthys TAGGAGGTCCTGCCTGCCCTGTGAC--A-C-CCAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAAGGCTTAACTGTCT-CCTCTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--C-T-C--CCTC-T-GA-CT-T-A-T-G-CAA-C--A--CC-CC-T--TA-A-TA----ACA--G-GA-C-CA-A--GC-T---AG--T-A--A-G--C-TACA-G--AAACTGTCTTTGGTTGGGGCGACCCCGGGGA-ACAA-AA-ACCCC-CC-ATG-AGG-AA-T-A-A--G-AGT--A-C-T----C--T-CCT-TAA-A-CCC-AGAG-CC-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Chologaster TAAGAGGTCCTGCCTGCCCTGTGAC--A-C-CTAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCTAAACTGTCT-CCTTTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATATAAACATAAGACGAGAAGACCCTGTGGAGCTTAAGA--C-T-A--CCTC-T-AA-CT-T-A-T-G-CAA-A--A--CT-CC-T--CA-A-CA----ACA--G-GA-C-TA-A--CT-T---AA--T-A--A-A--C-TATA-G--AAATTGTCTTTGGTTGGGGCGACCCCGGGGA-ACAA-AA-AACCC-CC-GTG-CAG-AA-T-A-G--G-TAC--A-C-C----C--T-CCT-TAA-A-CCC-AGAG-CC-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Aphredoderus TAAGAGGTCCCGCCTGCCCTGTGAC--A-T-CTAGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATAGAGACCTGTATGAATGGCAACACGAGGGCTTAACTGTCT-CCTTTCTCC-AGTCAGTGAAATTGATCCCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--C-A-C--CC-A-T-AA-CT-T-A-T-GCGAA-A--A--TT-CT-T--AA-ATCA----AAA--A-GA-A-AG-A--GC-TA--AA--T-A--A-G--C-CTTA-G--TAAATGTCTTTGGTTGGGGCGACCACGGGGG-ATAATAA-AGCCC-CC-ATG-CGG-AA-T-A-G--G-A-C--A---T----C--T-CCT-TAA-C-CTC-AGAG-CC-ACCGCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Coelorinchus TAAGAGGTCTCGCCTGCCCAGTGAC-TAAA-T--GTTTAACGGCCGTGGTATCTTAACCATGCGAAGGTAGCGTAATCATTTGTCTTTTAAATGAAGACCCGTATGAATGGCAAAACGAGGGCTTAACTGTCT-CCCCTCCCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGAGGATAAAATTATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CT-T-A--AA-A-TAA-CCC-T-G-T---AAA-A--T--AA-AC-T-TTG-A-TA----CAA--A-CA-C-AA-A---C-TT--AA----G--G-A--GTTTTATT--TAAATGTCTTTGGTTGGGGTGACCACGGGGT-AAAACAT-AACCC-CC-ACG-AAG-AT---TGG-GA-A-C--A---T--A-C--T-CCT-AAC-A-CCA-AGAG-AC-ACCCCTCTAAGCA-ACAAA-ATTTTTGA-C [...]
+Bregmaceros TGAGAGGTCCCGCCTGCCCAGTGAC-TA-T-AT-GTTAAACGGCCGTGGTATCTTAACCATGCTAAGGTAGCGAAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCCCCACGAGGGCTTGACTGTCT-CCTTCCCCC-AGTCAATGAAATTAAACTTCCCGTGCAGATGCGGGAATAAGCGCATAAGACGAGAAGACCCTTTGGAGCTTCAGA-CC-C-T--AA-A-TAAGTTA-T-G-T---TAA-A--C--AC-CC-T--T--C-AC----CGA--G-TA-A-AA-A---C-AT--AG--T-A--G-T----TTTATT--CAAGGGTCTTAGGTTGGGGCGACCACGGAGT-AAAATA--AACCCTCC-ACG-AAG-A----AGG-GG-C-C--T-C-TATAAG--C-CCT-AAA-T-CCC-CGAT-AA-TCACATCTAAGAA-ACAGA-ATTTCTGA-C [...]
+Stylephorus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGTTTTATCTTAACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCCCCCTCC-AGTCAATGAAACTGACCTCCCCGTGCAGAGGCGGGGATTATTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-G-TAGTGCA-T-G-T---CTA-A--A--AT-AC-T-AGA-A-AA----TAA--G-AA-A-AA-A---C-CC--AA--T-G--C-C--C-CCTACT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAA-AACCC-CC-ATG-TAG-AC---CGG-GG-A-A--A-C----A-T--C-CCT-AAA-A-CCC-AGAG-CA-ACCACTCTAAGAA-ACAAA-ACCTTTGA-C [...]
+Urophycis TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-A-TGTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCCCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATTAAAACATAAGACGAGAAGACCCTGTGGAGCTTAAGA-CC-T-A--AT-A-TAATTTA-T-G-T---ATA-A--T--AC-AC-T-AAA-A-TA----ACA--G-CT-A-AA-A---C-TC--AA--T-A--G-T--A-ATTATA--GAGGTGTCTTTGGTTGGGGCGACCGCGGGGT-ACAACAA-AACCC-CC-GCG-TGG-AT---TGG-GAGA----A-C-T----T--CTCCT-AGC-A-CCC-AGAG-CC-GCTACTCCAAGTA-ACAGA-ATTTCTGACT [...]
+Steindachneria TGAGAGGTCCAGCCTGCCCTGTGAC--A-T-A--GTTTAACGGCTGCGGTATTTTGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTCC-AGTCAATGAACTTGACCTCCCCGTGCAGAGGCGGGGATTAGTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-TC-T-A--GA-A-TAAACCA-T-G-T---AAA-A--C--AA-GC-T-GTA-A-TA----CCA--G-CA-T-AA-A---C-CA--AT--T-G--G-T--A-CCTATT--CAAATGTCTTTGGTTGGGGCAACCGCGGAGA-AAAATTT-AACCT-CC-ATG-TGG-AC---CGG-GG-G-T--A-C-T--A-C--C-CCT-AGA-A-CTC-AGAA-CC-ACCATTCCAAGAA-ACAGA-ACTTCTGACC [...]
+Macruronus TRRGAGGTCTCGCCTGCCCTGTGAC-TATT-A--GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGTGGACCTGTATGAACGGCATCACGAGGGCTTAACTGTCT-CCCCTCTCC-AGTCAATGAAATTAACCTCCCCGTGCAGAGGCGGGGATAAGAATATAAGACGAGAAGACCCTGTGGAGCTTTAAA-CC-T-A--AG-A-CAAACCA-T-T-C---CTA-G--T--AA-GC-T-GTG-A-TA----CCA--G-TATT-AAGA---C--T--AG--T-G--G-T--T-TTTGTT--GAAGTGTTTTTGGTTGGGGTGACCATGGGGA-AAAACAC-AACCC-CC-ACG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAC-A-CTG-AGAG-CC-CACACTCCAAGTA-ACAGA-ACTTCTGACC [...]
+Bathygadus TAAGAGGTCTCGCCTGCCCGGTGAC-TATA-T--GTTTAACGGCCGCGGTATTTTAACCGCGCGAAGGTAGCGTAATCATTTGTCTTTTAAATGAAGACCTGTATGAATGGTATTACGAGGGCTCAACTGTCT-CCCTTCTCC-AGTCAATGAAATTGACTTCCCCGTGCAGAGGCGGGGATATTAATATAAGACGAGAAGACCCTGTGGAGCTTAAGA-CC-T-A--AG-A-TAAGCCA-T-G-T---TCA-G--G--AA-TC-TAAAA-A-CA----TAA--G-TA-T-AA-A---C-TT--AG--T-G--G-C--A-TTTATT--GAAGTGTCTTCGGTTGGGGTGACCCTGGGGA-AAAACTT-AACCC-CC-AAG-TAG-AC---TGG-GT-A-C--A-T-T--G-T--C-TCT-AGA-A-CTC-AGAG-CC-CATACTCCAAGTA-ACAGA-ATATTTGA-C [...]
+Muraenolepis TAGGAGGTCCCGCCTGCCCTGTGAC-TAAT-A--GTTTAACGGCCGCGGTATTTTAACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCTTTTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAAGCACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAGCTA-C-G-T---TTA-A--C--AG-CC-T-GTA-A-AA----TCA--G-AA-A-TA-A---C-TT--AG--T-A--G-T--C-TTTATT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-C-T--A-T--C-CCT-AAT-A-CCA-AGGG-CC-TCCCCCCCAAGTA-ACAGA-ACTTCTGACC [...]
+Physiculus TAAGAGGTCCCGCCTGCCCTGTGAC-GAAA----GTTTAACGGCCGCGGTATTCTAACCGTGCGAAGGTAGCGTAATCACTTGTTTTTTAAATGGAGACCAGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCTTCTTT-AGTCAATGAAATTGACCTTCCCGTGCAGAGGCGGGAATTACTATATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAGTCA-C-A-T---TTA-A--C--AT-GC-T-TAA-A-CA----ACA--G-TA-A-AA-A---T-AT--AG--T-G--A-A--ACATTATT--GAAGTGTCTTTGGTTGGGGCGACCATGGGGT-AAAACAC-AACCC-CC-ATA-CGG-AC---TGG-GG-A-T--A-C-A--A-T--C-CCT-AAT-A-CCC-AGAG-CC-TCCGCTCCAAGTA-ACAGA-ATTTCTGA-C [...]
+Merluccius TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATCTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCTCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATATTTATATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-G-TAAACCA-C-G-T---TTA-A--T--GT-AC-T-AGA-ATTA----ATA--G-CA-A-AA-A---C-TT--AG--TGG--A-C--A-TTTATT--TAAGTGTCTTTGGTTGGGGCGACCGCGGAGT-AAAACAT-AACCT-CC-ATG-TGG-A----CGG-GG-A-T--A-C-T--T-T--C-CCT-AAA-A-CTC-AGAG-CC-TCCACTCCAAGCA-ACAGA-AATTCTGACC [...]
+Melanonus TAAGAGGTCCCGCCTGCCCACTGAC-TA-T-AT-GTTCAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCCCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATACCCCTATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAATTA-T-G-T---TCA-A--C--AC-TC-T-ACA-A-AA----CCA--G-TA-A-AA-A---C-TT--AA--T-A--A-C--A-TTTATT--CAAGTGTCTTTGGTTGGGGCGACCGAGGGGA-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAC-A-CTC-AGAG-CC-GCTACTCCAAGTA-ACAGA-AATTCTGACC [...]
+Raniceps TAAGAGGTCCCGCCTGCCCTGTGAC-TT-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCCCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATATTTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-G-TAAGCCA-T-G-T---TTA-G--T--AT-CC-T-GAG-A-TA----TCA--G-TA-A-AA-A---C-TT--AA--T-G--G-C--A-ATTATT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAT-A-CTC-AGAG-CC-GCTACTCCAAGTA-ACAGA-AATTCTGAC- [...]
+Trachyrincus TAAGAGGTCCCGCCTGCCCAGTGAC-TACA-T--GTTTAACGGCCGCAGTATTTTAACCGCGCGAAGGTAGCGTAATCACCTGTTTTTTAAATGAAGACCTGTATGAATGGCTCAACGAGGGCTTAACTGTCT-CCCTCCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATATTTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAGTCA-C-G-T---TTA-A--C--AT-TC-T-GTA-A-TA----TCA--G-TA-A-AA-A---C-TC--AG----C--G-A--CGATTATT--GAAGTGTCTTCGGTTGGGGCGACCCTGGGGA-AAAACAC-AACCC-CC-ATG-TGG-AC---TGG-GA-A-T--A-C-T--A-T--T-CCT-AAC-A-CTC-AGAG-CC-TCTACTCCAAGTA-ACAGA-AATTCTGA-C [...]
+Euclichthys TAAGAGGTCCCGCCTGCCCAGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAAATATATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T----AA-G-TAAATCA-C-G-T---TTA-A--C--AT-CC-T-AGA-A-CA----ATA--G-AA-T-AA-A---C-CT--AG--T-G--A-A--A-ATTATG--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAA-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T----G-T--A-T--C-CCT-AAC-A-CTC-AGAG-CC-TATACTCCAAGTA-ACAGA-AAATCTGACC [...]
+Synodus TAAGAGGTCCCGCCTGCCCTGTGAC-T--A-AT-GTTTAACGGCCGCGGTATCTTGACCGTGCGAAGGTAGCGCAATCACTTGTCCTTTAAATGGGGACCTGTATGAATGGCACAACGAGGGCTTAACTGTCT-CCCCCCTCC-TGTCAGTGAAACTGATCTCCCCGTGAAGAAGCGGGGATTCCACTACCAGACGAGAAGACCCTATGGAGCTTAAAA-CA---A--AA-G-A-GG-GC-C---T---ATA-T--A--AA-CC-A--A--G-GG--C-AGA--T-AA-A-C--AC-AG-CAGTTGTTTAG--T-T--C-CCT--CC-GTAGT-T-TTTGGTTGGGGCGACCGTGGAGA-AACAAAA-AACCC-CC-ATG-CAG-AA-C-AGG-A--T-T--A-C---TAGAA-C-CTT-A-A-A-CCC-AGAG-CC-ACAGCTCTAAGTA-TCAAA-ATATTTGA-- [...]
+Chlorophthalmus TAAGAGGTCCCGCCTGCCCAGTGACTTG-T-ATAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCCTTTAAATGGGGACCTGTATGAATGGCACGACGAGGGCTTAGCTGTCT-CCCCTATCC-TGTTAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CA---CTTAA-G-C-GA-CC-C-A-A---ATA-G--AGCAA-AC-T-CA--C-CA--C-AAA--T-GA-GCTG-AC-TC-CCGATG-GTAA--G-A--C-AC---CGTTTAGTGTCTTTGGTTGGGGCGACCGTGGGGA-AAAGAAA-AACCC-CC-ATG-AGG-AC-CTGGG-G--C-G--ACC---C--CC-C-CCC-ATA-G-CCG-AGAGCCC-ACCACTCGAAGCA-TCAGA-ACCTCTGA-C [...]
+Macroparalepis TAAGAGGTCCCGCCTGCCCTGTGACCCC-C-AAAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCCTTTAAATGAGGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCCCTGTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCTGGGATAAAACCATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CG---ATTAG-A-T-GA-CC-C-G-C---ATG-A--GGCCG--C-T--T--C-AA--C-ACA--A-TT-GGGG--CGAC-CCCTCA-GTGATTT-A--T-CCT--CATCCTATGTCTTTGGTTGGGGCGACCGTGGGGG-AAAGAAT-ATCCC-CC-ATGTAGG-AC-TGAAA-A--C-C--A-C---T--CC-T-TTT-ATA-G-CTA-AGAGCCT-ACCACTCGAAGCA-TCAGA-ATTTCTGA-C [...]
+Diaphus TAAGSGGTCCCGCCTGCCCWGTGAC-CA-T-GT-GTTCAACGGCCGCGGTATTCTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAAAGGCATCACGAGGGCTTGACTGTCT-CCCCTTTAA-GGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATACGCTCGTAAGACGAGAAGACCCTATGGAGCTTAAGA-CA-T-A--AG-G-C-GA-CC-C-A-C-G-TCA-A--A--AACCC-TCCC--C-CCT-TAAGA--G-GA-A-AT-G--AA-CA--AA-GT-G--G-G--C-CTCA-CC-GAAATGTCTTCGGTTGGGGCGACCGCGGGGA-AAGACCA-AACCC-CC-ACA-TGG-AT-T-AAG-A--C-C--ACA----A-TAGC-CTT-AAA-A-CCC-AGAC-CT-CCAAGTCAAATCA-ACAGA-ATTTCTGA-C [...]
+Monocentris TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACGACGAGGGCCTAACTGTCT-CCTTTTTCA-GGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATAACTACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CA-C-A--AA-G-C-AG-CC-C-A-C-G-TTA-A--G--AA-AC-C--CC-A-AA--C-AAG--G-AA-CTA--A--AC-TA--AG--TGA--C-G--C-CCTG-CC-AGAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAGACTA-AACCC-CC-ATG-TGGAAA-G-GGA-A--G-ACTA-C----C-C--T-CCT-ACA-G-CCA-AGAG-CC-ACTGCTCTAAGTA-ACAGA-ATTTCTGA-C [...]
+Brosmophycis TAAGAGGTCCCGCCTGCCCTGTGAC-AA-T-AC-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCACAACGAGGGCTTAACTGTCT-CCTTTCCCT-AGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATTAATACATAAGACGAGAAGACCCTATGGAGCTTTAGA-TACT-A--AA-A-C-AG-CC-C-A-T-G-TTA-A--A--GA-CC-C--CA-T-AA--T-AAA--G-GAGC-A--A--AC-TA--AA--T-G--G-C--C-CCTG-TC-CTAATATCTTTGGTTGGGGCGACCGCGGGGA-AATATTA-AACCC-CC-ATG-TGG-AA-T-GGG-A--G-C--A------C-C--T-CCC-CCAGAGCCA-AGAG-CA-ACAGCTCTAAGCA-ACAGA-ACATCTGA-C [...]
+Opsanus TAAGAAGTCCCGCCTGCCCCGTGAC--A-C-AA-GTTTAACGGCTGCAGTAATATAACTGTACAAAGGTAGCGTAATCACCTGTCTTTTAATTGAAGACCTGTATGAATGGCATCACGAGGATTTAACTGTCTCTACTTTTC--AATCAATGAAATTGTTTTTCCCGTGCAAAAACGGGAATATATCTATAAGACGAGAAGACCCTGTGGAGCTTTA-A--G-T-A--AC-C-C-AG----------G-----A--A--TG-TA-T--TA---AA----ACA----TA-C-A--T--TT-TA--CC--T-A--A-A--A-------C-TTAC--T-TTTGGTTGGGGCGACCATGAAGA-AAAAAAG-AACCT-TC-ATA-AGG-AA-C-GGA-A--G----A--------C--T-CCT-AAA-A-C-A-CGAA-CG-ACAGTTCTAATTA-ACAGA-ATTTCTGA-C [...]
+Chaunax TAAGAGGTCCCGCCTGCCCAGTGAC-TA-C-AA-GTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCATTTGTCTTTTAAATTAAGACCTGTATGAAAGGTGAGACGAGGGCTTAGCTGTCT-CCTCTCTC-CAGTCAATGAAATTGATCCCCCCGTGCAGAAGCGGGGATTTTAACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CACT-C--GG-G-C-AG-AC-T-A-T-G--TC-AAGT--AC-CC-C-TAA-T-AA----A-G----GT-GAA--A--ACAGAGTAT--G----C-T--A-CT-G-TC-CCAATGTCTTCGGTTGGGGCGACCATGGGGA-AATAAGA-AACCC-CCAAAG-TGG-AA-T-GGA-A--A-CAGA-CC-CTT-T--T-TCT-ACA-A-CTG-AGAG-TA-CCCCCTCTAGCTA-ACAGA-ACTTCTGA-C [...]
+Lycodes TAAGAGGTTCCGCCTGCCCTGTGAC-TA-T-TA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCTTTTTC-CAGTCAATGAAGTTGATCTTCCCGTGCAGAAGCGGGAATACAAACATAAGACGAGAAGACCCTATGAAGCTTTAGA-CACC-A--AG-A-C-AG-CT-C-A-T-G-TTA-AT-A--AC-CC-T-GAA-T-AA----A-G----GC-TTA--A--AC-CA-AAT--G-A--A-G--C-CT-G-TC-CGAATGTCTTTGGTTGGGGCGACCGCGGGGC-ATTAAAA-AACCC-CC-ACG-TGG-AA-T-GGG-A--G-C--A-C--C-C-C--T-CCT-ACA-A-CTA-AGAG-CC-ACAGCTCTAGTAA-ACAGA-AATTCTGA-C [...]
+Arcos TAGGAGGTCCCGCCTGCCCTGTGAC-TA-T-GG-GTTCAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCGAAACGAGGGCTCAACTGTCTCCCCCTTTT--AATCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATACCACCATAAGACGAGAAGACCCTGTGGAGCTTTAGA-TA-T-AT-AA-A-G-GG-AT-T-A-TAC-CAA-AT-T--TG-CC-T--TC-T-AA----ACA----GG-CTA--A--AC-TA--AT--T-A--ATA--T-CC-T-TT-TTGCTGTCTTTGGTTGGGGCGACCACGGGGA-AAAATAA-AACCC-CC-ACG-CGG-AT-A-AAA-A--G-A--A-C--C-CGC--T-TTT-ACAGA-GT--AGAG-CC-TCAGCTCT-ACAACACAGA-ACTTCTGA-C [...]
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster14/cmdline.txt b/tests/clustering/DNA_rcluster14/cmdline.txt
new file mode 100644
index 0000000..b1c4a64
--- /dev/null
+++ b/tests/clustering/DNA_rcluster14/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-max 1000 --rcluster-percent 10
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster14/partition_finder.cfg b/tests/clustering/DNA_rcluster14/partition_finder.cfg
new file mode 100644
index 0000000..92068bf
--- /dev/null
+++ b/tests/clustering/DNA_rcluster14/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = alignment.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G, GTR+I+G;
+model_selection = AICc;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+tRNAval_16S = 1-1436;
+28S = 1437-2147;
+ENC1_1 = 2149-2937\3;
+ENC1_2 = 2150-2937\3;
+ENC1_3 = 2148-2937\3;
+H3_1 = 2940-3270\3;
+H3_2 = 2938-3270\3;
+H3_3 = 2939-3270\3;
+RAG1_intron = 3271-3429;
+RAG1_1 = 3430-4027\3;
+RAG1_2 = 3431-4027\3;
+RAG1_3 = 3432-4027\3;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = rcluster;
diff --git a/tests/clustering/DNA_rcluster2/Caterino_2001.phy b/tests/clustering/DNA_rcluster2/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster2/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster2/cmdline.txt b/tests/clustering/DNA_rcluster2/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/DNA_rcluster2/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster2/partition_finder.cfg b/tests/clustering/DNA_rcluster2/partition_finder.cfg
new file mode 100644
index 0000000..dcb35b4
--- /dev/null
+++ b/tests/clustering/DNA_rcluster2/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+I+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster2/results.bin b/tests/clustering/DNA_rcluster2/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster2/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster3/Caterino_2001.phy b/tests/clustering/DNA_rcluster3/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster3/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster3/cmdline.txt b/tests/clustering/DNA_rcluster3/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/DNA_rcluster3/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster3/partition_finder.cfg b/tests/clustering/DNA_rcluster3/partition_finder.cfg
new file mode 100644
index 0000000..5b448bd
--- /dev/null
+++ b/tests/clustering/DNA_rcluster3/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+I+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-390\3;
+COI_2 = 30-390\3;
+COI_3 = 31-390\3;
+EF1a_1 = 2035-2340\3;
+EF1a_2 = 2036-2340\3;
+EF1a_3 = 2037-2340\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster3/results.bin b/tests/clustering/DNA_rcluster3/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster3/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster4/Caterino_2001.phy b/tests/clustering/DNA_rcluster4/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster4/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster4/cmdline.txt b/tests/clustering/DNA_rcluster4/cmdline.txt
new file mode 100644
index 0000000..ee527ab
--- /dev/null
+++ b/tests/clustering/DNA_rcluster4/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "1,1,1,1"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster4/partition_finder.cfg b/tests/clustering/DNA_rcluster4/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster4/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster4/results.bin b/tests/clustering/DNA_rcluster4/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster4/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster5/Caterino_2001.phy b/tests/clustering/DNA_rcluster5/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster5/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster5/cmdline.txt b/tests/clustering/DNA_rcluster5/cmdline.txt
new file mode 100644
index 0000000..7ea31ef
--- /dev/null
+++ b/tests/clustering/DNA_rcluster5/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "0,0,0,0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster5/partition_finder.cfg b/tests/clustering/DNA_rcluster5/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster5/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster5/results.bin b/tests/clustering/DNA_rcluster5/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster5/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster6/Caterino_2001.phy b/tests/clustering/DNA_rcluster6/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster6/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster6/cmdline.txt b/tests/clustering/DNA_rcluster6/cmdline.txt
new file mode 100644
index 0000000..11f888e
--- /dev/null
+++ b/tests/clustering/DNA_rcluster6/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "1000, 0.01, 0.003, 0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster6/partition_finder.cfg b/tests/clustering/DNA_rcluster6/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster6/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster6/results.bin b/tests/clustering/DNA_rcluster6/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster6/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster7/Caterino_2001.phy b/tests/clustering/DNA_rcluster7/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster7/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster7/cmdline.txt b/tests/clustering/DNA_rcluster7/cmdline.txt
new file mode 100644
index 0000000..0339783
--- /dev/null
+++ b/tests/clustering/DNA_rcluster7/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "-1000, 0.01, 0.003, 0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster7/partition_finder.cfg b/tests/clustering/DNA_rcluster7/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster7/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster7/results.bin b/tests/clustering/DNA_rcluster7/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster7/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster8/Caterino_2001.phy b/tests/clustering/DNA_rcluster8/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster8/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster8/cmdline.txt b/tests/clustering/DNA_rcluster8/cmdline.txt
new file mode 100644
index 0000000..1e62101
--- /dev/null
+++ b/tests/clustering/DNA_rcluster8/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent = "0"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster8/partition_finder.cfg b/tests/clustering/DNA_rcluster8/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster8/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster8/results.bin b/tests/clustering/DNA_rcluster8/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster8/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster9/Caterino_2001.phy b/tests/clustering/DNA_rcluster9/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/clustering/DNA_rcluster9/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/clustering/DNA_rcluster9/cmdline.txt b/tests/clustering/DNA_rcluster9/cmdline.txt
new file mode 100644
index 0000000..7a8a461
--- /dev/null
+++ b/tests/clustering/DNA_rcluster9/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent = "0.000001"
\ No newline at end of file
diff --git a/tests/clustering/DNA_rcluster9/partition_finder.cfg b/tests/clustering/DNA_rcluster9/partition_finder.cfg
new file mode 100644
index 0000000..9dc6d84
--- /dev/null
+++ b/tests/clustering/DNA_rcluster9/partition_finder.cfg
@@ -0,0 +1,24 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-100\3;
+COI_2 = 30-100\3;
+COI_3 = 31-100\3;
+EF1a_1 = 2335-2500\3;
+EF1a_2 = 2336-2500\3;
+EF1a_3 = 2337-2500\3;
+
+## SCHEMES ##
+[schemes]
+search = rcluster;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/clustering/DNA_rcluster9/results.bin b/tests/clustering/DNA_rcluster9/results.bin
new file mode 100644
index 0000000..79719e5
--- /dev/null
+++ b/tests/clustering/DNA_rcluster9/results.bin
@@ -0,0 +1 @@
+�]q(G���VM��G@�VM��G@�!�+|=G@��|Y2��e.
\ No newline at end of file
diff --git a/tests/clustering/__init__.py b/tests/clustering/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/clustering/prot_hcluster1/cmdline.txt b/tests/clustering/prot_hcluster1/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/prot_hcluster1/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/prot_hcluster1/concat_alignment.phy b/tests/clustering/prot_hcluster1/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_hcluster1/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_hcluster1/partition_finder.cfg b/tests/clustering/prot_hcluster1/partition_finder.cfg
new file mode 100644
index 0000000..33cdf62
--- /dev/null
+++ b/tests/clustering/prot_hcluster1/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = LG+G;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = hcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_hcluster1/results.bin b/tests/clustering/prot_hcluster1/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_hcluster1/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_hcluster2/cmdline.txt b/tests/clustering/prot_hcluster2/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/prot_hcluster2/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/prot_hcluster2/concat_alignment.phy b/tests/clustering/prot_hcluster2/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_hcluster2/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_hcluster2/partition_finder.cfg b/tests/clustering/prot_hcluster2/partition_finder.cfg
new file mode 100644
index 0000000..1bd9b28
--- /dev/null
+++ b/tests/clustering/prot_hcluster2/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = all;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = hcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_hcluster2/results.bin b/tests/clustering/prot_hcluster2/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_hcluster2/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_hcluster3/cmdline.txt b/tests/clustering/prot_hcluster3/cmdline.txt
new file mode 100644
index 0000000..2b20f9a
--- /dev/null
+++ b/tests/clustering/prot_hcluster3/cmdline.txt
@@ -0,0 +1 @@
+--raxml
\ No newline at end of file
diff --git a/tests/clustering/prot_hcluster3/concat_alignment.phy b/tests/clustering/prot_hcluster3/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_hcluster3/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_hcluster3/partition_finder.cfg b/tests/clustering/prot_hcluster3/partition_finder.cfg
new file mode 100644
index 0000000..4b4439a
--- /dev/null
+++ b/tests/clustering/prot_hcluster3/partition_finder.cfg
@@ -0,0 +1,22 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = allx;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-400;
+COII = 401-949;
+
+######## SCHEMES #########
+[schemes]
+search = hcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_hcluster3/results.bin b/tests/clustering/prot_hcluster3/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_hcluster3/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster1/cmdline.txt b/tests/clustering/prot_rcluster1/cmdline.txt
new file mode 100644
index 0000000..bf9f833
--- /dev/null
+++ b/tests/clustering/prot_rcluster1/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "1, 0, 100, egg"
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster1/concat_alignment.phy b/tests/clustering/prot_rcluster1/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_rcluster1/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_rcluster1/partition_finder.cfg b/tests/clustering/prot_rcluster1/partition_finder.cfg
new file mode 100644
index 0000000..074d780
--- /dev/null
+++ b/tests/clustering/prot_rcluster1/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = LG+G;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = rcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_rcluster1/results.bin b/tests/clustering/prot_rcluster1/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_rcluster1/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster2/cmdline.txt b/tests/clustering/prot_rcluster2/cmdline.txt
new file mode 100644
index 0000000..fba4096
--- /dev/null
+++ b/tests/clustering/prot_rcluster2/cmdline.txt
@@ -0,0 +1 @@
+--raxml --rcluster-percent 12 --weights "1,0,0,0"
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster2/concat_alignment.phy b/tests/clustering/prot_rcluster2/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_rcluster2/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_rcluster2/partition_finder.cfg b/tests/clustering/prot_rcluster2/partition_finder.cfg
new file mode 100644
index 0000000..b5f5320
--- /dev/null
+++ b/tests/clustering/prot_rcluster2/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = LG+I+G;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = rcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_rcluster2/results.bin b/tests/clustering/prot_rcluster2/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_rcluster2/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster3/cmdline.txt b/tests/clustering/prot_rcluster3/cmdline.txt
new file mode 100644
index 0000000..7ea31ef
--- /dev/null
+++ b/tests/clustering/prot_rcluster3/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "0,0,0,0"
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster3/concat_alignment.phy b/tests/clustering/prot_rcluster3/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_rcluster3/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_rcluster3/partition_finder.cfg b/tests/clustering/prot_rcluster3/partition_finder.cfg
new file mode 100644
index 0000000..985a94e
--- /dev/null
+++ b/tests/clustering/prot_rcluster3/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = LG+I+G;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = rcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_rcluster3/results.bin b/tests/clustering/prot_rcluster3/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_rcluster3/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster4/cmdline.txt b/tests/clustering/prot_rcluster4/cmdline.txt
new file mode 100644
index 0000000..7ea31ef
--- /dev/null
+++ b/tests/clustering/prot_rcluster4/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "0,0,0,0"
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster4/concat_alignment.phy b/tests/clustering/prot_rcluster4/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_rcluster4/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_rcluster4/partition_finder.cfg b/tests/clustering/prot_rcluster4/partition_finder.cfg
new file mode 100644
index 0000000..2a28076
--- /dev/null
+++ b/tests/clustering/prot_rcluster4/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = EGG;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = rcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_rcluster4/results.bin b/tests/clustering/prot_rcluster4/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_rcluster4/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster5/cmdline.txt b/tests/clustering/prot_rcluster5/cmdline.txt
new file mode 100644
index 0000000..7ea31ef
--- /dev/null
+++ b/tests/clustering/prot_rcluster5/cmdline.txt
@@ -0,0 +1 @@
+--raxml --weights "0,0,0,0"
\ No newline at end of file
diff --git a/tests/clustering/prot_rcluster5/concat_alignment.phy b/tests/clustering/prot_rcluster5/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/clustering/prot_rcluster5/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/clustering/prot_rcluster5/partition_finder.cfg b/tests/clustering/prot_rcluster5/partition_finder.cfg
new file mode 100644
index 0000000..29fde84
--- /dev/null
+++ b/tests/clustering/prot_rcluster5/partition_finder.cfg
@@ -0,0 +1,25 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = LG+I+G;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1;
+COII = 2;
+EF1a1 = 3;
+EF1a2 = 4;
+EF1a3 = 5;
+
+######## SCHEMES #########
+[schemes]
+search = rcluster;
+
+#user schemes listed below - only used if 'search = user'
diff --git a/tests/clustering/prot_rcluster5/results.bin b/tests/clustering/prot_rcluster5/results.bin
new file mode 100644
index 0000000..8d6f4b3
--- /dev/null
+++ b/tests/clustering/prot_rcluster5/results.bin
@@ -0,0 +1 @@
+�]q(G������*G@����*G@�Q�A�
G@���͈%e.
\ No newline at end of file
diff --git a/tests/clustering/test_clustering.py b/tests/clustering/test_clustering.py
new file mode 100644
index 0000000..a13ccee
--- /dev/null
+++ b/tests/clustering/test_clustering.py
@@ -0,0 +1,86 @@
+import os
+import pytest
+from partfinder import main, util, analysis, config
+
+# Get the Errors all into the local space
+from partfinder.config import ConfigurationError
+from partfinder.util import PartitionFinderError
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+test_description = """
+DNA_hcluster1 | success |
+DNA_hcluster2 | success |
+DNA_hcluster3 | PartitionFinderError |
+DNA_hcluster4 | success | --weights "1,1,1,1"
+DNA_hcluster5 | PartitionFinderError | --weights "0,0,0,0"
+DNA_hcluster6 | success | --weights "1000,0.01,0.003,0"
+DNA_hcluster7 | PartitionFinderError | --weights "-1000,0.01,0.003,0"
+DNA_rcluster1 | success |
+DNA_rcluster2 | success |
+
+DNA_rcluster3 | success |
+
+DNA_rcluster4 | success | --weights "1,1,1,1"
+DNA_rcluster5 | PartitionFinderError | --weights "0,0,0,0"
+DNA_rcluster6 | success | --weights "1000, 0.01, 0.003, 0"
+DNA_rcluster7 | ConfigurationError | --weights "-1000, 0.01, 0.003, 0"
+DNA_rcluster8 | success | --rcluster-percent 0
+DNA_rcluster9 | success | --rcluster-percent 0.000001
+DNA_rcluster10 | success | --rcluster-percent 99.999999
+DNA_rcluster11 | success | --rcluster-percent 100.00
+DNA_rcluster12 | ConfigurationError | --rcluster-percent 100.001
+DNA_rcluster13 | ConfigurationError | --rcluster-percent -0.001
+DNA_rcluster14 | success | --rcluster-max 1000 --rcluster-percent 10 -p 1
+
+prot_hcluster1 | success |
+prot_hcluster2 | success |
+prot_hcluster3 | success |
+prot_rcluster1 | ConfigurationError | --weight "1, 0, 100, egg"
+prot_rcluster2 | success | --rcluster-percent 12 --weight "1,0,0,0"
+prot_rcluster3 | PartitionFinderError | --weight "0,0,0,0"
+prot_rcluster4 | PartitionFinderError |
+prot_rcluster5 | success |
+"""
+
+# Turn the text above into a container of info about the tests
+test_container = {}
+for line in test_description.split('\n'):
+ line = line.strip()
+ if not line:
+ continue
+ name, res, cmdline = [x.strip() for x in line.split('|')]
+ if name[:3] == "DNA":
+ kind = "DNA"
+ else:
+ kind = "protein"
+ if res == 'success':
+ error = None
+ elif res[:5] == 'xfail':
+ error = 'xfail', res[5:].strip()
+ else:
+ # Get the Exception from the local space (must be imported)
+ error = locals()[res]
+
+ test_container[name] = error, kind, cmdline
+
+
+def pytest_generate_tests(metafunc):
+ # This function feeds the output of the above function into the tests below
+ if 'folder_name' in metafunc.fixturenames:
+ # Send it sorted order
+ k = test_container.keys()
+ k.sort()
+ metafunc.parametrize('folder_name', k)
+
+# The actual test function
+def test_clustering(folder_name):
+ full_path = os.path.join(HERE, folder_name)
+ error, kind, cmdline = test_container[folder_name]
+ if error is None:
+ main.call_main(kind, '"%s" --raxml %s' % (full_path, cmdline))
+ elif type(error) == type((0, 0)):
+ pytest.xfail(error[1])
+ else:
+ with pytest.raises(error):
+ main.call_main(kind, '"%s" --raxml %s' % (full_path, cmdline))
diff --git a/tests/clustering/tests.txt b/tests/clustering/tests.txt
new file mode 100644
index 0000000..dd78bbc
--- /dev/null
+++ b/tests/clustering/tests.txt
@@ -0,0 +1,36 @@
+
+Name brlens models selection search outcome
+-----------------------------------------------------------------------
+DNA_hcluster1 linked all bic hcluster success
+DNA_hcluster2 unlinked GTR+I+G bic hcluster success
+DNA_hcluster3 linked JC bic hcluster failure - JC model shouldn't work because it's not in RAxML
+DNA_hcluster4 linked GTR+G bic hcluster success (weight = "1,1,1,1")
+DNA_hcluster5 linked GTR+G bic hcluster success (weight = "0,0,0,0")
+DNA_hcluster6 linked GTR+G bic hcluster success (weight = "1000, 0.01, 0.003, 0")
+DNA_hcluster7 linked GTR+G bic hcluster failure - negative weights (weight = "-1000, 0.01, 0.003, 0")
+
+
+DNA_rcluster1 linked all bic rcluster success
+DNA_rcluster2 unlinked GTR+I+G bic rcluster success
+DNA_rcluster3 linked GTR+I+G bic rcluster success *very small subsets
+
+DNA_rcluster4 linked GTR+G bic hcluster success (weight = "1,1,1,1")
+DNA_rcluster5 linked GTR+G bic hcluster success (weight = "0,0,0,0")
+DNA_rcluster6 linked GTR+G bic hcluster success (weight = "1000, 0.01, 0.003, 0")
+DNA_rcluster7 linked GTR+G bic hcluster failure - negative weights (weight = "-1000, 0.01, 0.003, 0")
+DNA_rcluster8 linked GTR+G bic hcluster success (rcluster-percent = "0")
+DNA_rcluster9 linked GTR+G bic hcluster success (rcluster-percent = "0.000001")
+DNA_rcluster10 linked GTR+G bic hcluster success (rcluster-percent = "99.999999")
+DNA_rcluster11 linked GTR+G bic hcluster success (rcluster-percent = "100.00")
+DNA_rcluster12 linked GTR+G bic hcluster failure (rcluster-percent = "100.001")
+DNA_rcluster13 linked GTR+G bic hcluster failure (rcluster-percent = "-0.001")
+
+
+Prot_hcluster1 linked all_protein bic hcluster success
+Prot_hcluster2 unlinked LG+G bic hcluster success
+Prot_hcluster3 linked allx bic hcluster success (this is to test if we can parse output from all of RAxMLs types of model)
+Prot_rcluster1 linked all_protein bic rcluster failure (weight = "1, 0, 100, egg")
+Prot_rcluster2 linked LG+I+G bic rcluster success (rcluster-percent = 12; weight = "1,0,0,0")
+Prot_rcluster3 linked LG+I+G bic rcluster success (weight = "0,0,0,0")
+Prot_rcluster4 linked EGG bic rcluster failure ("EGG is not a model")
+Prot_rcluster5 linked LG+I+G bic rcluster success *very small subsets*
diff --git a/tests/full_analysis/DNA1/Caterino_2001.phy b/tests/full_analysis/DNA1/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA1/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA1/partition_finder.cfg b/tests/full_analysis/DNA1/partition_finder.cfg
new file mode 100644
index 0000000..0b06528
--- /dev/null
+++ b/tests/full_analysis/DNA1/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA1/results.bin b/tests/full_analysis/DNA1/results.bin
new file mode 100644
index 0000000..a468ba9
Binary files /dev/null and b/tests/full_analysis/DNA1/results.bin differ
diff --git a/tests/full_analysis/DNA2/Caterino_2001.phy b/tests/full_analysis/DNA2/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA2/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA2/partition_finder.cfg b/tests/full_analysis/DNA2/partition_finder.cfg
new file mode 100644
index 0000000..3d33f18
--- /dev/null
+++ b/tests/full_analysis/DNA2/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA2/results.bin b/tests/full_analysis/DNA2/results.bin
new file mode 100644
index 0000000..93e2f10
Binary files /dev/null and b/tests/full_analysis/DNA2/results.bin differ
diff --git a/tests/full_analysis/DNA3-analysis.zip b/tests/full_analysis/DNA3-analysis.zip
new file mode 100644
index 0000000..0bd22b4
Binary files /dev/null and b/tests/full_analysis/DNA3-analysis.zip differ
diff --git a/tests/full_analysis/DNA3/Caterino_2001.phy b/tests/full_analysis/DNA3/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA3/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA3/partition_finder.cfg b/tests/full_analysis/DNA3/partition_finder.cfg
new file mode 100644
index 0000000..bb33e12
--- /dev/null
+++ b/tests/full_analysis/DNA3/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA3/results.bin b/tests/full_analysis/DNA3/results.bin
new file mode 100644
index 0000000..1730cab
Binary files /dev/null and b/tests/full_analysis/DNA3/results.bin differ
diff --git a/tests/full_analysis/DNA4/Caterino_2001.phy b/tests/full_analysis/DNA4/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA4/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA4/partition_finder.cfg b/tests/full_analysis/DNA4/partition_finder.cfg
new file mode 100644
index 0000000..2c00115
--- /dev/null
+++ b/tests/full_analysis/DNA4/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aicc;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA4/results.bin b/tests/full_analysis/DNA4/results.bin
new file mode 100644
index 0000000..1730cab
Binary files /dev/null and b/tests/full_analysis/DNA4/results.bin differ
diff --git a/tests/full_analysis/DNA5/Caterino_2001.phy b/tests/full_analysis/DNA5/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA5/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA5/partition_finder.cfg b/tests/full_analysis/DNA5/partition_finder.cfg
new file mode 100644
index 0000000..8ca57d8
--- /dev/null
+++ b/tests/full_analysis/DNA5/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA5/results.bin b/tests/full_analysis/DNA5/results.bin
new file mode 100644
index 0000000..fe7ecf6
Binary files /dev/null and b/tests/full_analysis/DNA5/results.bin differ
diff --git a/tests/full_analysis/DNA6/Caterino_2001.phy b/tests/full_analysis/DNA6/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA6/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA6/partition_finder.cfg b/tests/full_analysis/DNA6/partition_finder.cfg
new file mode 100644
index 0000000..d22135b
--- /dev/null
+++ b/tests/full_analysis/DNA6/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = greedy;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA6/results.bin b/tests/full_analysis/DNA6/results.bin
new file mode 100644
index 0000000..a468ba9
Binary files /dev/null and b/tests/full_analysis/DNA6/results.bin differ
diff --git a/tests/full_analysis/DNA7/Caterino_2001.phy b/tests/full_analysis/DNA7/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA7/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA7/partition_finder.cfg b/tests/full_analysis/DNA7/partition_finder.cfg
new file mode 100644
index 0000000..2b4e23f
--- /dev/null
+++ b/tests/full_analysis/DNA7/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = aicc;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA7/results.bin b/tests/full_analysis/DNA7/results.bin
new file mode 100644
index 0000000..e011cdd
Binary files /dev/null and b/tests/full_analysis/DNA7/results.bin differ
diff --git a/tests/full_analysis/DNA8/Caterino_2001.phy b/tests/full_analysis/DNA8/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/DNA8/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/DNA8/partition_finder.cfg b/tests/full_analysis/DNA8/partition_finder.cfg
new file mode 100644
index 0000000..0947397
--- /dev/null
+++ b/tests/full_analysis/DNA8/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = greedy;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/DNA8/results.bin b/tests/full_analysis/DNA8/results.bin
new file mode 100644
index 0000000..6b18782
Binary files /dev/null and b/tests/full_analysis/DNA8/results.bin differ
diff --git a/tests/full_analysis/__init__.py b/tests/full_analysis/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/full_analysis/kmeans1/alignment.phy b/tests/full_analysis/kmeans1/alignment.phy
new file mode 100755
index 0000000..6af9cb7
--- /dev/null
+++ b/tests/full_analysis/kmeans1/alignment.phy
@@ -0,0 +1 @@
+8 17092
Chl__pygerythrus_gb_ZA GTCTACGTAGCTTAAA-CCACCCCAAAGCAAGACACTGAAAATGCCTAGATGGATTCACACATCCCATAGACAAACAGGTTTGGTCCTAGCCTTTCTATTGACCTTTAGCAAGATTACACATGCAAGCCTCCCCGCCCCAGTGAAGACGCCCTACAAATCA-CCATGACTAAGAGGAGTGAGTATCAAGCACGCATA-TGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTACACCAAGGGTCGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCGAGCCAATAGAGACCGGCGTAGAGGGTGTTTTAGACCC-----AACCTAATTAAAGCTAAACCCCACCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACCTCTG [...]
C__dryas_R_CD GTCTACGTAGCTTAAACCCACTCCAAAGCAAGACACTGAAAATGCCTAGATGGATTCACACATCCCATAGACAAATAGGTTTGGTCCTGGCCTTTCTATTGACCTTTAGCAAGATTACACATGCAAGCCTCCCCGCCCCAGTGAAGACGCCCTACAAATCA-CCATGACTAAGAGGAGTGAGTATCAAGCACGCATA-TGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGTAATAAACGAAAGTTTAACTAAGCTATGCTACACCAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCAAGCCAATAGAGACCGGCGTAGAGAGTGTTTTAGGCCC-----AATCTAAATAAAGCTAAACCCCACCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACCCCTGAACACACAA [...]
C__c__ngottoensis_R_CF GTCTACGTAGCTTAAACCCA-CCCAAAGCAAGACACTGAAAATGCCTAGATGGACTCACACACCCCGTAGACAAATAGGTTTGGTCCTGGCCTTTCTATTGACCCTTAGCAAGATTACACATGCAAGCATCCCCACCCCAGTGAAGACGCCCTACAAATCACCCACGACTAAGAGGAGTGAGTATCAAGCACGCACA-CGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTACATCAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCGAGCCAATAGAGACCGGCGTAGAGAGTGTTTTAGATCT-----AATCCAAT-AAAGCTAAACCCCGTCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACTTCTG [...]
E__patas_DPZ GTCTACGTAGCTTAAACC-A-CCCAAAGCAAGACACTGAAAATGCCTAGATGGACTCACATATCCCATAGACAAATAGGTTTGATCCTGGCCTTTCTATTGACCCTTAGCAAGATTACACATGCAAGCATCCACACTCCAGTGAAGACGCCCTACAAATCA-CCACGACTAAGAGGAGCAAGTATCAAGCACGCACA-TGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTATAT-CAGGGTTGGTCAATCTCGTGCCAGCCACCGCGGCCATACGATTAACCCGAGCCAATAGAGACCGGCGTAAAGAGTGTTTTAGATCC-----AGCCTAAT-AAAGCTAAACCCCGTCTAAACTGTAAAATCCTAGCCAACATAAAATAAACTACGAAAGTGGCTTTAAAATTTCTGAACACACAAT [...]
A__nigroviridis_N_CG GTCTGTGTAGCTTAAATCCA-CTTAAAGCAAGACACTGAAAATGCCTAGACGGGCTCACATACCCCGCAGACAAATAGGTTTGGTCCTGGCCTTCCTATTGACTCTTAGCAAGACTACACATGCAAGCATCCCCACCCCAGTGAAGACACCCTGTAAAATCACTATGACTTACAGGAGTAAGTATCAAGCACGCACA-TGCAGCTCAAAACACTTTGCCTAGCCACACCCCCACGGGAAACAGCAGTGACAAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTATATCAAGGGTTGGTTAATTTCGTGCCAGCCACCGCGGCCATACGATTGACCCGAGCCAATAGGGATCGGCGTAGAGAGTGTTTTAGATCT-----AATACAAT-AAAGCTAAACCCCATCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACTTCTGAA [...]
M__ogouensis_R_CM GCCCATGTAGCTTAAACCCA-CCCAAAGCAAAGTACTGAAAATACCTAGATGGG-TCACGCACCCCATGGACAAACAGGCTTGGTCCTGGCCTTTCTATTGGCCCTTAGCAAGATTACACATGCAAGCATCCCCGCTCCAGTGAAGACGCCCTACAAATCG-CCACGACTAGGAGGAGCAAGTATCAAGCACGCACA-CGCAGCTCAAGACACTTCGCCTAGCCACACCCCCACGGGAGACAGCAGTGACAAACCTTTGGCAATAAACGAAAGTTTAACCAAGCTATGCTATATCAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCGAGCCAATAGAGATCGGCGTAAAGGGTGTTTTAGATCT-----TATACAAT-AAAGCTAAATCCTATCTAAACCGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAATTTCTGAACAC [...]
T__gelada_B_ET GTTTATGTAGCTTAAACCCGC-CTAAAGCAAGACACTGAAAATGCCTAGATGGGTCCACACACCCCATAAACAAATAGGCTTGGTCCTGGCCTTTCTATTGACTCTTAGCAAGATTACACATGCAAGTATCCTCGCTCCGGTGAAGACGCCCCCCCTATCA-ACATGACCGAGAGGAGCAAGCATCAAGCACGCACA-TGCAGCTCAAAACGCTTTGCCTAGCCACACCCCCACGGGAGACAGCAGTGACAAATCTTTAGCAATGAACGAAAGTTTAACTAAGCTATGCTATACTAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTTACACGATTAACCCTAGCCAATAGAAATCGGCGTAGAGGGTGTTTTGGATCT-----AATCTAAT-AAAGCTAAACCACACCTAAACTGTAAAACTCTAGCTAACGTAAAATAAACTACGAAGGTGGCTTTATAACTTCTGAACACACA [...]
Proc__badius_gb GTTTATGTAGCTTAA--CAGATCCAAAGCAAGACACTGAAAATGCCTAGATGGGTTCACAC--CCCATAAACAAATAGGTTTGGTCCTGGCCTTTCTATTAACTCGTAGCAAGATTACACATGCAAGCATCCCCGCTCCAGTGAAGACGCCCTACAAATCA-CCATGATAAGAAGGAGTAAGTATCAAGCACGCCTAGTGCAGCTCAAGACACTTTGCTTAGCCACACCCCCACGGGAAACAGCAGTGATTAATATTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTAC-TATAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTGACCCAAGCTAATAGGCACCGGCGTAAAGAGTGTTTTAGATCAACATAAACCCAAT-AAAGCTAAACTATGTCTAAACTGTAAAATTCTAGCCAATGTAAAATAAACTACGAAAGTGGCTTTAAAAAATCTGAATACAC [...]
\ No newline at end of file
diff --git a/tests/full_analysis/kmeans1/partition_finder.cfg b/tests/full_analysis/kmeans1/partition_finder.cfg
new file mode 100755
index 0000000..5dfc23b
--- /dev/null
+++ b/tests/full_analysis/kmeans1/partition_finder.cfg
@@ -0,0 +1,17 @@
+## ALIGNMENT FILE ##
+alignment = alignment.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+G, GTR, GTR+G;
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+all_data = 1-15460;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = kmeans;
diff --git a/tests/full_analysis/kmeans_fast/alignment.phy b/tests/full_analysis/kmeans_fast/alignment.phy
new file mode 100755
index 0000000..6af9cb7
--- /dev/null
+++ b/tests/full_analysis/kmeans_fast/alignment.phy
@@ -0,0 +1 @@
+8 17092
Chl__pygerythrus_gb_ZA GTCTACGTAGCTTAAA-CCACCCCAAAGCAAGACACTGAAAATGCCTAGATGGATTCACACATCCCATAGACAAACAGGTTTGGTCCTAGCCTTTCTATTGACCTTTAGCAAGATTACACATGCAAGCCTCCCCGCCCCAGTGAAGACGCCCTACAAATCA-CCATGACTAAGAGGAGTGAGTATCAAGCACGCATA-TGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTACACCAAGGGTCGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCGAGCCAATAGAGACCGGCGTAGAGGGTGTTTTAGACCC-----AACCTAATTAAAGCTAAACCCCACCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACCTCTG [...]
C__dryas_R_CD GTCTACGTAGCTTAAACCCACTCCAAAGCAAGACACTGAAAATGCCTAGATGGATTCACACATCCCATAGACAAATAGGTTTGGTCCTGGCCTTTCTATTGACCTTTAGCAAGATTACACATGCAAGCCTCCCCGCCCCAGTGAAGACGCCCTACAAATCA-CCATGACTAAGAGGAGTGAGTATCAAGCACGCATA-TGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGTAATAAACGAAAGTTTAACTAAGCTATGCTACACCAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCAAGCCAATAGAGACCGGCGTAGAGAGTGTTTTAGGCCC-----AATCTAAATAAAGCTAAACCCCACCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACCCCTGAACACACAA [...]
C__c__ngottoensis_R_CF GTCTACGTAGCTTAAACCCA-CCCAAAGCAAGACACTGAAAATGCCTAGATGGACTCACACACCCCGTAGACAAATAGGTTTGGTCCTGGCCTTTCTATTGACCCTTAGCAAGATTACACATGCAAGCATCCCCACCCCAGTGAAGACGCCCTACAAATCACCCACGACTAAGAGGAGTGAGTATCAAGCACGCACA-CGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTACATCAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTAACCCGAGCCAATAGAGACCGGCGTAGAGAGTGTTTTAGATCT-----AATCCAAT-AAAGCTAAACCCCGTCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACTTCTG [...]
E__patas_DPZ GTCTACGTAGCTTAAACC-A-CCCAAAGCAAGACACTGAAAATGCCTAGATGGACTCACATATCCCATAGACAAATAGGTTTGATCCTGGCCTTTCTATTGACCCTTAGCAAGATTACACATGCAAGCATCCACACTCCAGTGAAGACGCCCTACAAATCA-CCACGACTAAGAGGAGCAAGTATCAAGCACGCACA-TGCAGCTCAAAACACTTTGCTCAGCCACACCCCCACGGGAAACAGCAGTGACAAATCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTATAT-CAGGGTTGGTCAATCTCGTGCCAGCCACCGCGGCCATACGATTAACCCGAGCCAATAGAGACCGGCGTAAAGAGTGTTTTAGATCC-----AGCCTAAT-AAAGCTAAACCCCGTCTAAACTGTAAAATCCTAGCCAACATAAAATAAACTACGAAAGTGGCTTTAAAATTTCTGAACACACAAT [...]
A__nigroviridis_N_CG GTCTGTGTAGCTTAAATCCA-CTTAAAGCAAGACACTGAAAATGCCTAGACGGGCTCACATACCCCGCAGACAAATAGGTTTGGTCCTGGCCTTCCTATTGACTCTTAGCAAGACTACACATGCAAGCATCCCCACCCCAGTGAAGACACCCTGTAAAATCACTATGACTTACAGGAGTAAGTATCAAGCACGCACA-TGCAGCTCAAAACACTTTGCCTAGCCACACCCCCACGGGAAACAGCAGTGACAAACCTTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTATATCAAGGGTTGGTTAATTTCGTGCCAGCCACCGCGGCCATACGATTGACCCGAGCCAATAGGGATCGGCGTAGAGAGTGTTTTAGATCT-----AATACAAT-AAAGCTAAACCCCATCTAAACTGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAACTTCTGAA [...]
M__ogouensis_R_CM GCCCATGTAGCTTAAACCCA-CCCAAAGCAAAGTACTGAAAATACCTAGATGGG-TCACGCACCCCATGGACAAACAGGCTTGGTCCTGGCCTTTCTATTGGCCCTTAGCAAGATTACACATGCAAGCATCCCCGCTCCAGTGAAGACGCCCTACAAATCG-CCACGACTAGGAGGAGCAAGTATCAAGCACGCACA-CGCAGCTCAAGACACTTCGCCTAGCCACACCCCCACGGGAGACAGCAGTGACAAACCTTTGGCAATAAACGAAAGTTTAACCAAGCTATGCTATATCAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTCATACGATTAACCCGAGCCAATAGAGATCGGCGTAAAGGGTGTTTTAGATCT-----TATACAAT-AAAGCTAAATCCTATCTAAACCGTAAAATCCTAGCTAACATAAAATAAACTACGAAAGTGGCTTTAAAATTTCTGAACAC [...]
T__gelada_B_ET GTTTATGTAGCTTAAACCCGC-CTAAAGCAAGACACTGAAAATGCCTAGATGGGTCCACACACCCCATAAACAAATAGGCTTGGTCCTGGCCTTTCTATTGACTCTTAGCAAGATTACACATGCAAGTATCCTCGCTCCGGTGAAGACGCCCCCCCTATCA-ACATGACCGAGAGGAGCAAGCATCAAGCACGCACA-TGCAGCTCAAAACGCTTTGCCTAGCCACACCCCCACGGGAGACAGCAGTGACAAATCTTTAGCAATGAACGAAAGTTTAACTAAGCTATGCTATACTAAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGTTACACGATTAACCCTAGCCAATAGAAATCGGCGTAGAGGGTGTTTTGGATCT-----AATCTAAT-AAAGCTAAACCACACCTAAACTGTAAAACTCTAGCTAACGTAAAATAAACTACGAAGGTGGCTTTATAACTTCTGAACACACA [...]
Proc__badius_gb GTTTATGTAGCTTAA--CAGATCCAAAGCAAGACACTGAAAATGCCTAGATGGGTTCACAC--CCCATAAACAAATAGGTTTGGTCCTGGCCTTTCTATTAACTCGTAGCAAGATTACACATGCAAGCATCCCCGCTCCAGTGAAGACGCCCTACAAATCA-CCATGATAAGAAGGAGTAAGTATCAAGCACGCCTAGTGCAGCTCAAGACACTTTGCTTAGCCACACCCCCACGGGAAACAGCAGTGATTAATATTTAGCAATAAACGAAAGTTTAACTAAGCTATGCTAC-TATAGGGTTGGTCAATTTCGTGCCAGCCACCGCGGCCATACGATTGACCCAAGCTAATAGGCACCGGCGTAAAGAGTGTTTTAGATCAACATAAACCCAAT-AAAGCTAAACTATGTCTAAACTGTAAAATTCTAGCCAATGTAAAATAAACTACGAAAGTGGCTTTAAAAAATCTGAATACAC [...]
\ No newline at end of file
diff --git a/tests/full_analysis/kmeans_fast/partition_finder.cfg b/tests/full_analysis/kmeans_fast/partition_finder.cfg
new file mode 100755
index 0000000..fe26670
--- /dev/null
+++ b/tests/full_analysis/kmeans_fast/partition_finder.cfg
@@ -0,0 +1,17 @@
+## ALIGNMENT FILE ##
+alignment = alignment.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+G, GTR, GTR+G;
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+all_data = 1-200;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = kmeans;
diff --git a/tests/full_analysis/kmeans_fast/results.bin b/tests/full_analysis/kmeans_fast/results.bin
new file mode 100644
index 0000000..5f79492
Binary files /dev/null and b/tests/full_analysis/kmeans_fast/results.bin differ
diff --git a/tests/full_analysis/prot1/concat_alignment.phy b/tests/full_analysis/prot1/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot1/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot1/partition_finder.cfg b/tests/full_analysis/prot1/partition_finder.cfg
new file mode 100644
index 0000000..94f1a63
--- /dev/null
+++ b/tests/full_analysis/prot1/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = JTT, LG+G, WAG+I+G+F, LG+G+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = all;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot1/results.bin b/tests/full_analysis/prot1/results.bin
new file mode 100644
index 0000000..dda49cf
Binary files /dev/null and b/tests/full_analysis/prot1/results.bin differ
diff --git a/tests/full_analysis/prot2/concat_alignment.phy b/tests/full_analysis/prot2/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot2/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot2/partition_finder.cfg b/tests/full_analysis/prot2/partition_finder.cfg
new file mode 100644
index 0000000..bb8ee27
--- /dev/null
+++ b/tests/full_analysis/prot2/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = WAG, WAG+G, LG+I+G+F, JTT+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = all;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot2/results.bin b/tests/full_analysis/prot2/results.bin
new file mode 100644
index 0000000..d7b2084
--- /dev/null
+++ b/tests/full_analysis/prot2/results.bin
@@ -0,0 +1 @@
+�]q(G���� �G@��� �G@���E��G@�>�b�vxe.
\ No newline at end of file
diff --git a/tests/full_analysis/prot3/concat_alignment.phy b/tests/full_analysis/prot3/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot3/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot3/partition_finder.cfg b/tests/full_analysis/prot3/partition_finder.cfg
new file mode 100644
index 0000000..ab1c8dd
--- /dev/null
+++ b/tests/full_analysis/prot3/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = WAG, WAG+G, LG+I+G+F, JTT+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = aic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = all;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot3/results.bin b/tests/full_analysis/prot3/results.bin
new file mode 100644
index 0000000..f3b0122
--- /dev/null
+++ b/tests/full_analysis/prot3/results.bin
@@ -0,0 +1 @@
+�]q(G����+�G@����+�G@��>�o�G@��#��e.
\ No newline at end of file
diff --git a/tests/full_analysis/prot4/concat_alignment.phy b/tests/full_analysis/prot4/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot4/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot4/partition_finder.cfg b/tests/full_analysis/prot4/partition_finder.cfg
new file mode 100644
index 0000000..0b34c4c
--- /dev/null
+++ b/tests/full_analysis/prot4/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = WAG, WAG+G, LG+I+G+F, JTT+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = aicc;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = all;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot4/results.bin b/tests/full_analysis/prot4/results.bin
new file mode 100644
index 0000000..f3b0122
--- /dev/null
+++ b/tests/full_analysis/prot4/results.bin
@@ -0,0 +1 @@
+�]q(G����+�G@����+�G@��>�o�G@��#��e.
\ No newline at end of file
diff --git a/tests/full_analysis/prot5/concat_alignment.phy b/tests/full_analysis/prot5/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot5/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot5/partition_finder.cfg b/tests/full_analysis/prot5/partition_finder.cfg
new file mode 100644
index 0000000..9864dc6
--- /dev/null
+++ b/tests/full_analysis/prot5/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = WAG, WAG+G, LG+I+G+F, JTT+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = user;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot5/results.bin b/tests/full_analysis/prot5/results.bin
new file mode 100644
index 0000000..94a9b24
--- /dev/null
+++ b/tests/full_analysis/prot5/results.bin
@@ -0,0 +1 @@
+�]q(G��
0O�G@�
0O�G@�� j��G@�>����e.
\ No newline at end of file
diff --git a/tests/full_analysis/prot6/concat_alignment.phy b/tests/full_analysis/prot6/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot6/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot6/partition_finder.cfg b/tests/full_analysis/prot6/partition_finder.cfg
new file mode 100644
index 0000000..8084656
--- /dev/null
+++ b/tests/full_analysis/prot6/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = linked;
+
+######## MODELS OF EVOLUTION ###########
+models = JTT, LG+G, WAG+I+G+F, LG+G+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = greedy;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot6/results.bin b/tests/full_analysis/prot6/results.bin
new file mode 100644
index 0000000..dda49cf
Binary files /dev/null and b/tests/full_analysis/prot6/results.bin differ
diff --git a/tests/full_analysis/prot7/concat_alignment.phy b/tests/full_analysis/prot7/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot7/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot7/partition_finder.cfg b/tests/full_analysis/prot7/partition_finder.cfg
new file mode 100644
index 0000000..77da648
--- /dev/null
+++ b/tests/full_analysis/prot7/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = JTT, LG+G, WAG+I+G+F, LG+G+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = aicc;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = all;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot7/results.bin b/tests/full_analysis/prot7/results.bin
new file mode 100644
index 0000000..03b299c
Binary files /dev/null and b/tests/full_analysis/prot7/results.bin differ
diff --git a/tests/full_analysis/prot8/concat_alignment.phy b/tests/full_analysis/prot8/concat_alignment.phy
new file mode 100644
index 0000000..2779636
--- /dev/null
+++ b/tests/full_analysis/prot8/concat_alignment.phy
@@ -0,0 +1,11 @@
+10 949
+AD00P068 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXXXXNNETXXSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPMFTGLMMNSYLLKIQFILXXXXXXXXXXXXXXXXXXXXXXXXXXXXXMXLSWNIISSLGSYMSFISMMMMLMIIWESMIXQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIXXXX [...]
+SY03A501 SLMMLISSMIVENGAGTGWTVYPPLSSNIAHSGSSVDLTIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWSVGITAMLLLLSLPILAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATMYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFSGFIHWYPLFTGLMMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMMIIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+SY03A503 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMPLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMMWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIYWYPLFTGLKMNSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMFLSWNIISSLGSYMSFISMMMMIMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLMFYMMLMMFWNKFINRFLLEGQMIEXXXXXXXXXXLIF [...]
+TDA99Q985 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNMSFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXPXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGSQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIVSSLGSYMSFISMLLMMMIIWESMIKKRLILFSLNMSSSIEWLQNTPPNEHSYNELPILNNFMATWSNLNFQNSVSPLMEQIIFFNDHSLIILIMITMLLSYMMLSMFWNKFINRXLLEGQMXXXXXXXXXXIILIF [...]
+TDA99Q986 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGXXXXXXXXXXXXXXISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYXVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXDXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGXMSXLIXXXXXXXXXXX [...]
+UK99W804 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXHIXSQESXKKETFGSLXMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMFIGVXXXXXXXXXXXXXXXXXXXXXXXXXXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXXXXXF [...]
+UK99W805 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNMNTSFFDPAGGGDPILYQHLFXXXXXXXXXXXXXXXXXIISHIISQESGKKEXFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMXSYLLKIQFILMFIGVNXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
+YJ02Q703 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLFNIXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIWTILPAIILIF [...]
+ZD99S303 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQXXXXXXXXXXXXXXXXXXXGIISHIISQESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQLILMFIGXXXXXXXXXXXXXXXXXXXXXXXXDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIXLIXXXXXXXXXXX [...]
+ZD99S305 SLMLLISSSIVENGAGTGWTVYPPLSSNIAHSGSSVDLAIFSLHLAGISSILGAINFITTIINMKVNNLFFDQMSLFIWAVGITALLLLLSLPVLAGAITMLLTDRNLNTSFFDPAGGGDPILYQHLFWFFGHPXXXXXXXXXXXXXXXXXXXESGKKETFGSLGMIYAMLAIGLLGFIVWAHHMFTVGMDIDTRAYFTSATMIIAVPTGIKIFSWLATIYGTQINYSPSMLWSLGFIFLFAVGGLTGVILANSSIDITLHDTYYVVAHFHYVLSMGAIFAIFGGFIHWYPLFTGLMMNSYLLKIQFILMXXXXXXXXXXXXXXXXXXXXXXXXXXPDMXLSWNIISSLGSYMSFISMMMMMMIIWESMIKQRLILFSLNMSSSIEWLQNTPPNEHSYNELPILSNFMATWSNLNFQNSVSPLMEQIIFFHDHSLIILIMITMLLSYMMLSMFWNKFINRFLLEGQMIELIXXXXXXIILIF [...]
diff --git a/tests/full_analysis/prot8/partition_finder.cfg b/tests/full_analysis/prot8/partition_finder.cfg
new file mode 100644
index 0000000..dd5e626
--- /dev/null
+++ b/tests/full_analysis/prot8/partition_finder.cfg
@@ -0,0 +1,27 @@
+######## ALIGNMENT FILE ###########
+alignment = concat_alignment.phy;
+
+######## BRANCHLENGTHS ###########
+branchlengths = unlinked;
+
+######## MODELS OF EVOLUTION ###########
+models = JTT, LG+G, WAG+I+G+F, LG+G+F;
+
+# model selection: "AIC", "AICc", "BIC"
+model_selection = bic;
+
+######## PARTITIONS ###########
+[data_blocks]
+COI = 1-100;
+COII = 101-200;
+EF1a1 = 201-300;
+EF1a2 = 301-400;
+EF1a3 = 401-500;
+
+######## SCHEMES #########
+[schemes]
+search = greedy;
+
+#user schemes listed below - only used if 'search = user'
+all_together = (COI, COII, EF1a1, EF1a2, EF1a3);
+all_separate = (COI) (COII) (EF1a1) (EF1a2) (EF1a3);
\ No newline at end of file
diff --git a/tests/full_analysis/prot8/results.bin b/tests/full_analysis/prot8/results.bin
new file mode 100644
index 0000000..03b299c
Binary files /dev/null and b/tests/full_analysis/prot8/results.bin differ
diff --git a/tests/full_analysis/rerun01/Caterino_2001.phy b/tests/full_analysis/rerun01/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun01/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun01/partition_finder.cfg b/tests/full_analysis/rerun01/partition_finder.cfg
new file mode 100644
index 0000000..bf0d2c4
--- /dev/null
+++ b/tests/full_analysis/rerun01/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun02/Caterino_2001.phy b/tests/full_analysis/rerun02/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun02/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun02/partition_finder.cfg b/tests/full_analysis/rerun02/partition_finder.cfg
new file mode 100644
index 0000000..bb33e12
--- /dev/null
+++ b/tests/full_analysis/rerun02/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun03/Caterino_2001.phy b/tests/full_analysis/rerun03/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun03/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun03/partition_finder.cfg b/tests/full_analysis/rerun03/partition_finder.cfg
new file mode 100644
index 0000000..2c00115
--- /dev/null
+++ b/tests/full_analysis/rerun03/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aicc;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun04/Caterino_2001.phy b/tests/full_analysis/rerun04/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun04/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun04/partition_finder.cfg b/tests/full_analysis/rerun04/partition_finder.cfg
new file mode 100644
index 0000000..b4debd1
--- /dev/null
+++ b/tests/full_analysis/rerun04/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = greedy;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun05/Caterino_2001.phy b/tests/full_analysis/rerun05/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun05/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun05/partition_finder.cfg b/tests/full_analysis/rerun05/partition_finder.cfg
new file mode 100644
index 0000000..8ca57d8
--- /dev/null
+++ b/tests/full_analysis/rerun05/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun06/Caterino_2001.phy b/tests/full_analysis/rerun06/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun06/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun06/partition_finder.cfg b/tests/full_analysis/rerun06/partition_finder.cfg
new file mode 100644
index 0000000..e72b169
--- /dev/null
+++ b/tests/full_analysis/rerun06/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC+G, HKY+I, GTR+I+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun07/Caterino_2001.phy b/tests/full_analysis/rerun07/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun07/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun07/partition_finder.cfg b/tests/full_analysis/rerun07/partition_finder.cfg
new file mode 100644
index 0000000..0a43f1f
--- /dev/null
+++ b/tests/full_analysis/rerun07/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G, JC+I+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun08/Caterino_2001.phy b/tests/full_analysis/rerun08/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun08/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun08/partition_finder.cfg b/tests/full_analysis/rerun08/partition_finder.cfg
new file mode 100644
index 0000000..8267f12
--- /dev/null
+++ b/tests/full_analysis/rerun08/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, HKY+I+G, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun09/Caterino_2001.phy b/tests/full_analysis/rerun09/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun09/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun09/partition_finder.cfg b/tests/full_analysis/rerun09/partition_finder.cfg
new file mode 100644
index 0000000..3d33f18
--- /dev/null
+++ b/tests/full_analysis/rerun09/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun10/Caterino_2001.phy b/tests/full_analysis/rerun10/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun10/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun10/partition_finder.cfg b/tests/full_analysis/rerun10/partition_finder.cfg
new file mode 100644
index 0000000..e3f9bd5
--- /dev/null
+++ b/tests/full_analysis/rerun10/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun11/Caterino_2001.phy b/tests/full_analysis/rerun11/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun11/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun11/partition_finder.cfg b/tests/full_analysis/rerun11/partition_finder.cfg
new file mode 100644
index 0000000..f671e4d
--- /dev/null
+++ b/tests/full_analysis/rerun11/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = greedy;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun12/Caterino_2001.phy b/tests/full_analysis/rerun12/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun12/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun12/partition_finder.cfg b/tests/full_analysis/rerun12/partition_finder.cfg
new file mode 100644
index 0000000..95aebec
--- /dev/null
+++ b/tests/full_analysis/rerun12/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = aicc;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun13/Caterino_2001.phy b/tests/full_analysis/rerun13/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun13/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun13/partition_finder.cfg b/tests/full_analysis/rerun13/partition_finder.cfg
new file mode 100644
index 0000000..62b71d0
--- /dev/null
+++ b/tests/full_analysis/rerun13/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION ##
+models = all;
+model_selection = aicc;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun14/Caterino_2001.phy b/tests/full_analysis/rerun14/Caterino_2001.phy
new file mode 100644
index 0000000..6c3eb64
--- /dev/null
+++ b/tests/full_analysis/rerun14/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 AAAAAAAAAAAAAAAAAAAAAAAAAATAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun14/partition_finder.cfg b/tests/full_analysis/rerun14/partition_finder.cfg
new file mode 100644
index 0000000..bf0d2c4
--- /dev/null
+++ b/tests/full_analysis/rerun14/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun15/Caterino_2001.phy b/tests/full_analysis/rerun15/Caterino_2001.phy
new file mode 100644
index 0000000..0622071
--- /dev/null
+++ b/tests/full_analysis/rerun15/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+I.changed.thisone ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun15/partition_finder.cfg b/tests/full_analysis/rerun15/partition_finder.cfg
new file mode 100644
index 0000000..bf0d2c4
--- /dev/null
+++ b/tests/full_analysis/rerun15/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun16/Caterino_2001.phy b/tests/full_analysis/rerun16/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun16/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun16/partition_finder.cfg b/tests/full_analysis/rerun16/partition_finder.cfg
new file mode 100644
index 0000000..e985dd4
--- /dev/null
+++ b/tests/full_analysis/rerun16/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-709\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun17/Caterino_2001.phy b/tests/full_analysis/rerun17/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun17/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun17/partition_finder.cfg b/tests/full_analysis/rerun17/partition_finder.cfg
new file mode 100644
index 0000000..2102628
--- /dev/null
+++ b/tests/full_analysis/rerun17/partition_finder.cfg
@@ -0,0 +1,25 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+added = 800-900;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/full_analysis/rerun18/Caterino_2001.phy b/tests/full_analysis/rerun18/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun18/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun18/partition_finder.cfg b/tests/full_analysis/rerun18/partition_finder.cfg
new file mode 100644
index 0000000..fce43af
--- /dev/null
+++ b/tests/full_analysis/rerun18/partition_finder.cfg
@@ -0,0 +1,23 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
diff --git a/tests/full_analysis/rerun19/Caterino_2001_ooh.phy b/tests/full_analysis/rerun19/Caterino_2001_ooh.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun19/Caterino_2001_ooh.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun19/partition_finder.cfg b/tests/full_analysis/rerun19/partition_finder.cfg
new file mode 100644
index 0000000..57846cf
--- /dev/null
+++ b/tests/full_analysis/rerun19/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001_ooh.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = all;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun20/Caterino_2001.phy b/tests/full_analysis/rerun20/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/full_analysis/rerun20/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun20/partition_finder.cfg b/tests/full_analysis/rerun20/partition_finder.cfg
new file mode 100644
index 0000000..0a4d291
--- /dev/null
+++ b/tests/full_analysis/rerun20/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2, EF1a_3, this_one_doesnt_exist);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/rerun21/Caterino_2001.phy b/tests/full_analysis/rerun21/Caterino_2001.phy
new file mode 100644
index 0000000..b43e2bf
--- /dev/null
+++ b/tests/full_analysis/rerun21/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 AAAAAAAA------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/full_analysis/rerun21/partition_finder.cfg b/tests/full_analysis/rerun21/partition_finder.cfg
new file mode 100644
index 0000000..0e7b29e
--- /dev/null
+++ b/tests/full_analysis/rerun21/partition_finder.cfg
@@ -0,0 +1,28 @@
+## ALIGNMENT FILE ##
+alignment = Caterino_2001.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = JC, JC+I, HKY, HKY+I+G, GTR, GTR+G;
+model_selection = bic;
+
+## DATA BLOCKS ##
+[data_blocks]
+COI_1 = 29-700\3;
+COI_2 = 30-700\3;
+COI_3 = 31-700\3;
+EF1a_1 = 2335-2800\3;
+EF1a_2 = 2336-2800\3;
+EF1a_3 = 2337-2800\3;
+
+## SCHEMES ##
+[schemes]
+search = user;
+
+#user schemes, only evalulated if schemes = 'user' or 'greedy'
+single_partition = (COI_1, COI_2, COI_3, EF1a_1, EF1a_2);
+by_gene = (COI_1, COI_2, COI_3) (EF1a_1, EF1a_2, EF1a_3);
+by_codon = (COI_1, EF1a_1) (COI_2, EF1a_2) (COI_3, EF1a_3);
+by_gene_codon = (COI_1) (COI_2) (COI_3) (EF1a_1) (EF1a_2) (EF1a_3);
diff --git a/tests/full_analysis/test_full.py b/tests/full_analysis/test_full.py
new file mode 100644
index 0000000..80c6dca
--- /dev/null
+++ b/tests/full_analysis/test_full.py
@@ -0,0 +1,64 @@
+import os
+import pytest
+from partfinder import main, util, analysis, config
+from zipfile import ZipFile
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+organise_tests = {
+ "dna" : ["DNA%d" % n for n in range(1, 9)],
+ "prot" : ["prot%d" % n for n in range(1, 9)],
+ "rerun_success" : ["rerun%02d" % int(n) for n in "1 2 3 4 5 6 7 8".split()],
+ "rerun_pf_error" : ["rerun%02d" % int(n) for n in "9 10 11 12 13 16 17 20 21".split()],
+ "rerun_ana_error" : ["rerun%02d" % int(n) for n in "14 15".split()],
+ "rerun_conf_error" : ["rerun%02d" % int(n) for n in "18 19".split()],
+}
+
+
+def pytest_generate_tests(metafunc):
+ # This function feeds the output of the above function into the tests below
+ for test_type, folders in organise_tests.items():
+ if test_type in metafunc.fixturenames:
+ metafunc.parametrize(test_type, folders)
+
+
+def test_dna(dna):
+ full_path = os.path.join(HERE, dna)
+ main.call_main("DNA", '--compare "%s"' % full_path)
+
+
+def test_prot(prot):
+ full_path = os.path.join(HERE, prot)
+ main.call_main("protein", '--compare "%s"' % full_path)
+
+
+def load_rerun(pth):
+ dna3 = ZipFile(os.path.join(HERE, 'DNA3-analysis.zip'))
+ dna3.extractall(pth)
+
+
+def test_rerun_success(rerun_success):
+ full_path = os.path.join(HERE, rerun_success)
+ load_rerun(full_path)
+ main.call_main("DNA", '"%s"' % full_path)
+
+
+def test_rerun_pf_error(rerun_pf_error):
+ full_path = os.path.join(HERE, rerun_pf_error)
+ load_rerun(full_path)
+ with pytest.raises(util.PartitionFinderError):
+ main.call_main("DNA", '"%s"' % full_path)
+
+
+def test_rerun_analysis_error(rerun_ana_error):
+ full_path = os.path.join(HERE, rerun_ana_error)
+ load_rerun(full_path)
+ with pytest.raises(analysis.AnalysisError):
+ main.call_main("DNA", '"%s"' % full_path)
+
+
+def test_rerun_config_error(rerun_conf_error):
+ full_path = os.path.join(HERE, rerun_conf_error)
+ load_rerun(full_path)
+ with pytest.raises(config.ConfigurationError):
+ main.call_main("DNA", '"%s"' % full_path)
diff --git a/tests/full_analysis/tests.txt b/tests/full_analysis/tests.txt
new file mode 100644
index 0000000..c8b441a
--- /dev/null
+++ b/tests/full_analysis/tests.txt
@@ -0,0 +1,79 @@
+Test descriptions
+
+Name brlens models selection search outcome
+-------------------------------------------------------------------
+Prot1 linked all_protein bic all success
+Prot2 unlinked selection* bic all success
+Prot3 linked selection* aic all success
+Prot4 linked selection* aicc all success
+Prot5 linked selection* bic user success
+Prot6 linked all_protein bic greedy success
+Prot7 unlinked all_protein aicc all success
+Prot8 unlinked all_protein bic greedy success
+
+DNA1 linked all bic all success
+DNA2 unlinked selection* bic all success
+DNA3 linked selection* aic all success
+DNA4 linked selection* aicc all success
+DNA5 linked selection* bic user success
+DNA6 linked all bic greedy success
+DNA7 unlinked all aicc all success
+DNA8 unlinked all bic greedy success
+
+rerun01 linked selection* bic all success (this is a direct rerun)
+rerun02 linked selection* aic all success (just changed selection to aic)
+rerun03 linked selection* aicc all success (just changed selection to aicc)
+rerun04 linked selection* bic greedy success (changed search to greedy)
+rerun05 linked selection* bic user success (changed search to user)
+rerun06 linked selection2** bic user success (new set of models)
+rerun07 linked selection3*** bic user success (added one extra model)
+rerun08 linked selection4**** bic user success (removed three models)
+
+rerun09 unlinked selection bic all failure (shouldn't be able to switch to unlinked after linked, the subsets will need to be deleted and re-analysed)
+rerun10 unlinked selection aic all failure (shouldn't be able to switch to unlinked after linked, the subsets will need to be deleted and re-analysed)
+rerun11 unlinked selection aic greedy failure (shouldn't be able to switch to unlinked after linked, the subsets will need to be deleted and re-analysed)
+rerun12 unlinked selection aicc user failure (shouldn't be able to switch to unlinked after linked, the subsets will need to be deleted and re-analysed)
+rerun13 unlinked all aicc user failure (shouldn't be able to switch to unlinked after linked, the subsets will need to be deleted and re-analysed)
+
+rerun14 linked selection bic all failure (I edited a sequence in the original alignment)
+rerun15 linked selection bic all failure (I edited a spp name in the original alignment)
+rerun16 linked selection bic all failure (I edited a data_block definition to change the boundaries)
+rerun17 linked selection bic all failure (I added a data_block)
+rerun18 linked selection bic all failure (I removed a data_block - this could work in theory but right now we have it conservatively set up to fail, this is OK in my opinion)
+rerun19 linked selection bic all failure (I changed the alignment filename, but the alignment itself is identical to the original. Again, this is conservative but OK)
+rerun20 linked selection bic user failure (I screwed up the user definitions to include a data_block that doesn't exist)
+rerun21 linked selection bic user failure (I screwed up the user definitions to exclude a data_block that does exist)
+
+D N A 5 linked selection bic user success (A copy of DNA5 but with stupid spaces in the filename)
+
+
+
+^
+all reruns start with all the files from DNA3 in there. This lets us test
+various things about loading in .cfg files with changes, added or subtracted
+models, changed alignments etc.
+
+*
+Protein models for the selection
+WAG, WAG+G, LG+I+G+F, JTT+F
+
+DNA models for the selection
+JC, JC+I, HKY, HKY+I+G, GTR, GTR+G
+
+**
+selection 2 has no models in common with selection
+JC+G, HKY+I, GTR+I+G
+
+***
+selection 3 adds one model to the original selection
+JC, JC+I, HKY, HKY+I+G, GTR, GTR+G, JC+I+G
+
+****
+selection 4 removes three models from the original selection
+JC, HKY+I+G, GTR+G
+
+Notes
+-----
+
+rerun9-13 are just various combinations to check that we always spot the
+changed .cfg file if we switch to unlinked brlens
diff --git a/tests/kmeans/Grande_2013/README.yaml b/tests/kmeans/Grande_2013/README.yaml
new file mode 100755
index 0000000..8de602c
--- /dev/null
+++ b/tests/kmeans/Grande_2013/README.yaml
@@ -0,0 +1,23 @@
+study:
+ reference: "Grande T, Borden WC, Smith WL (2013) Limits and relationships of Paracanthopterygii: A molecular framework for evaluating past morphological hypotheses. Mesozoic Fishes 5: 385-418. ISBN:978-3-89937-159-8"
+ DOI: NA
+
+dataset:
+ DOI: dx.doi.org/10.5061/dryad.k4m8t
+ license:
+ type: CC0
+ notes: ""
+ mitochondrial: yes
+ nuclear: yes
+ chloroplast: no
+ datatype: dna
+ number of taxa: 65
+ number of sites: 4027
+ number of data blocks: 12
+ used for tree inference: yes
+ study clade:
+ latin: "Paracanthopterygii"
+ english: "paracanthopterygian fish"
+ notes: ""
+
+notes: "The ms does not have a DOI, but it has an ISBN: ISBN:978-3-89937-159-8. The data blocks in this dataset were inferred with reference to the readme text associated with the dataset on dryad. Codon positions in each coding gene may not correspond with each other (i.e. '1' is not necessarily 1st codon position)."
\ No newline at end of file
diff --git a/tests/kmeans/Grande_2013/alignment.phy b/tests/kmeans/Grande_2013/alignment.phy
new file mode 100755
index 0000000..faa8d95
--- /dev/null
+++ b/tests/kmeans/Grande_2013/alignment.phy
@@ -0,0 +1,66 @@
+65 4027
+Maurolicus TAAGAGGTCCCGCCTGCCCAGTGAC-CA-T-GT-GTTCAACGGCCGCGGTATTTTAACCGTGCAAAGGTAGCGCAATCACTTGTCTCTTAAATAGAGACCTGTATGAATGGCACAACGAGGGCTCACCTGTCT-CCTCCTCCC-AGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAACACCCCCATAAGACGAGAAGACCCCATGGAACTTTAGA-CAC--T--AG-A-C-AA-CG-C-ACT-T-TTC-AT-T--C--CC----T--C-CT--T-TCT--C-GA-G-CG----AC-C---AC-GTGC--C-G--C-CCTG-TC-TCCTTGTCTTTGGTTGGGGTGACCCCGGAGA-ATAATGA-AACCT-CC-CCA-AGA-AA-C-AAG-A--G-C--A-C------CA-C-TCTCACA-A-CTA-AG-G-CCAACAACCCCAAGTA-CCAGA-ACCTCTGA-T [...]
+Lota TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAATTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AG-G-TAAGTCA-C-G-T---TTA-A--T--AT-AC-T-AGA-A-TA----ACA--G-TA-A-AA-A---C-TT--AG--T-G--A-T--A-TTTATC--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAT-A-CTC-AGAG-CC-TCTACTCCAAGTA-ACAGA-AATTCTGACT [...]
+Gadus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCATCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAATTACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--AA-G-TAAGTCA-C-G-T---TTA-A--C--AT-GC-T-GTG-A-TA----ACA--G-TA-A-AA-A---C-TT--AG--T-G--A-T--A-TTTACT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAT-A-CTC-AGAG-CC-TCTACTCCAAGTA-ACAGA-AATTCTGACT [...]
+Gaidropsarus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCCCTCC-AATCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAGTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAATTCA-C-GTT---TTA-A--T--AC-CC-T-GTT-A-TA----CCA--G-TA-A-AA-A---C-TT--AG--T-T--T-T--A-CTTATT--GAAGTGTCTTTGGTTGGGGCGACCACGGGGA-AAAATAT-AACCC-CC-ATG-AAG-AC---CGG-GG-A-T--A-C-T--A-T--C-CCT-AAT-A-CTC-AGAGCTT-TCTACTCCAAGTA-ACAGA-AATTCTGACT [...]
+Zu TAAGAGGCCACGCCTGCCCGGTGAC-TA-G-AA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAAAGGCGAGACGAGGGCAAAACTGTCT-CCCTTCTCA-TGTCAATGAAACTGATTTCCCCGTGCAGAAGCGGGGATGCAGTCACAAGACGAGAAGACCCTGTGGAGCTTTAGA--C-T-T--TA-G---TG--A-G-C-TTGCC-C-A--A--A--GT-A--T--A-AACCCCAAC--T-AT-ATAA-A--AA-CA--C---G-GC-T-A--C-CCTC-CCCTAAATGTCTTTGGTTGGGGCGACCGCGGAGATAA-AC-TAAACCA-CC-GCG-TGG-A--TAGGG-G--G-T-TA-A----C-C----CCT-ATA-A-TTA-AGAG-CT-ACAGCTCTATATA-TCAGG-ATTCCTGA-C [...]
+Trachipterus TAGGAGGCCACGCCTGCCCGGTGAC-TA-A-AA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCGAAACGAGGGCGAAACTGTCT-CCCCCCTTA-GGTCAATGAAACTGATCTCCCCGTGCAGAAGCGGGGATAGACCCACAAGACGAGAAGACCCTATGGAGCTTGAGA--C-T-T--TA-A---GG--A-G-C-CTGCC-C-T--A--A--GC-T--T--T-AACTT-AAT--T-GA-A-TG-A--AC-CC--C---G-GC-T-T--C-CCTC-CCCCAAATGTCTTTGGTTGGGGCGACTGCGGAGATAATAC-T-AACCC-CC-GCG-TGG-A--T-TGG-G--G----A-C----T-C----CCT-ATA-A-TCT-AGAG-CT-ACGGCTCTAAATA-TCAGA-ATTTCTGA-C [...]
+Regalecus TAAGAGGCCCCGCCTGCCCGGTGAC--G-A-AA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAAAGGCGACACGAGGGCAAATCTGTCT-CCCCCCTCC-AGTCAATGAAACTGATCTCCCCGTGCAGAAGCGGGGATACAACCACAAGACGAGAAGACCCTGTGGAGCTTCAGA--C-T-T--TG-G---TA--A-G-C-CTGCCTC-A--A-CC--CC-T--C--T-GA--C-AAA--G-GA-G-GGTT--AA-CA--C---A-GCAT-C--C-CCTT-ATTTAAATGTCTTTGGTTGGGGCGACCACGGAGATAATTT-T-AACCC-CC-GCG-GGG-A----TAG-G--G----A-C-T--T-T----CCT-ATA-A-CCC-AGAG-CT-ACAGCTCTAAGTG-TCAAG-ACTCTTGA-C [...]
+Lophotus TAGGAGG-CCCGCCTGCCCGGTGAC-TA-T-TA-GTTTAACGGCCGCGGTATTATGACCGTGCAAAGGTAGCGTAATCACTTGTCCTTTAAATAGGGACTAGTATGAATGGCGAAACGAGGGTGTAACTGTCT-CCCCCATCC-GGTCAATGAAACTGATCTCCCCGTGCAGAAGCGGGGATGAACACACAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-C--TG-G---AGT-A-T-A-C-CCCTT-T--T--C--CC-T--C--A-TA--T-AAA--G-TT-T-GG-A--AA-CTC-TG--G-GTGT-A--C-CCTC-CCAAGACTGTCTTTGGTTGGGGCGACCGCGGAGAGAACAC-T-ACCCC-CC-GCG-TGG-A--TGAAGTG--A----A-C-A--A-C----TTT-TTA-A-CCT-AGAG-CT-ACACCTCTAAGTG-TCAGA-ATATATGG-C [...]
+Ijimaia TAAGAGGTCCCGCCTGCCCTGTGAC-AA-T-TA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATTACGAGGGCTTAGCTGTCT-CCTTGCCCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACACCATAAGACGAGAAGACCCTGTGGAGCTTTAAATTA---T--AA-G-T-AG-AC-T-G-T-G-TTA-AT-A--CG-CC----A--A-AA--T-AAA-GG-AA-A-CT-AA-AC-CA--AA--TAG----A--C-ACTA-CT-TTAATATTTTTGGTTGGGGCGACCACGGGGG-ACAAATA-AGCCC-CC-ACG-AGG-AC-C-AGG-A----A--A-A----T-CT-T-CCT-AAA-A-CCA-AGAG-CT-ACAGCTCTAAGAA-ACAGA-ACTTCTGA-C [...]
+Coccorella TAAGAGGTCCTGCCTGCCCGGTGACTCA-A-AAAGTTAAACGGCCGCAGTATCTTAACTGTGCGAAGGTAGCGCAATCACTTGTCCTTTAATTGAGGACCTGTATGAATGGCAAGACGAGGGCTTAGCTGTCT-CCCCTGCCC-CGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGTTAACCCTATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA---ACCAA-A-C-GC-CT-C-A-C---ATA-A--GACAG-CC-T--A--A-AA--G-AAA--A-AA-GCTG--C-CC-ATCTTA-GTGA--C-A--C-CCT-CCGGTTTATGTCTTTGGTTGGGGCGACCGTGGGGA-AAAGAAA-ACCCC-CC-ATG-AAG-ACGTTAAA-G--A-C--T-C---T---C-T-TTT-ATA-A-CCA-AGAGCCT-ACTACTCAAAGTA-TCAGACACCTCTGA-C [...]
+Lampris TAAGAGGTCCCGCCTGCCCCGTGAC-AA-T-A--GTTTAACGGCCGCGGTATTCTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCACCACGAGGACTTAGCTGTCT-CCCCTCTCC-CGTCAGTAAAATTGACCTACCCGTGCAGAGGCGGGTACACCCCCACAAGACGAGAAGACCCTGTGGAGCTTTAGG-CC-CAA--GA-A---AG--AGG-A---C-ATC-A--A--G---C----C------------A----GA-A-AC-A--GC-CA--CA--G-CC-T-A--T-CTT--TC-CCAATGCCTTTGGTTGGGGCGACCACGGAGATAAAAC-A-AACCC-CC-GCG-TGG-AC-C-GAG-A--G----A-C-C--T-C--T-CTT-AGA-A-CTA-AGAG-CC-ACCCCTCCAAGCA-CCAGA-ACATCTGA-C [...]
+Velifer TAAGAGGCACCGCCTGCCCTGTGAC-TT-T-AT-GTTTAACGGCCGCGGTATCCTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCTCTCT-AGTCAGTAAAACTGATCTCCCCGTGCAGAAGCGGGGTTGCCCACACAAGACGAGAAGACCCTGTGGAGCTTTAGA-TA-T-A--AA-G---AG--GGGCACCT-TAAG-A--A--G-TCC----C--G-TA----AAA--G-GA-ACCCAA--TC-CC--CA--GTGC-A-C--T-CCT--TCTCGAATATCTTTGGTTGGGGCGACCGCGGGGA-CAAAC-AGAACCC-CC-ACG-AGG-AC-T-AAG-A--G-T--A-C-C--C-C--T-CCT-AAA-A-CCA-AGAG-CC-ACCACTCTAAGTA-CTAGA-ACATCTAA-C [...]
+Benthosema TAAGAGGTCCCGCCTGCCCAGTGACTAA-T-ATAGTTAAATGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACTGGTATGAACGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTAA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATATACTCGTAAGACGAGAAGACCCTATGGAGCTTAAGA-TA-TAA--AGTT-C-AA-CC-C-A-C-G-TCA-A--A--CA-CC-T-------CC--T-AAA--A-G--A-AT-A--AA-CA--AA-AT-G--A-A--C-CTTG-CT-GATATATCTTCGGTTGGGGCGACCACGGGGA-AAGACAA-AACCC-CC-ACA-TGG-AC-C-GGG-G--C-A--CCC----A-CA-C-CCT-AGA-A-CAT-AGAC-CC-ACAGGTCAAATCA-ACAGC-ACTTCTGA-C [...]
+Neoscopelus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAAAGGCACCACGAGGGCTTAACTGTCT-CCCCTTTAG-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACCCCGTAAGACGAGAAGACCCTATGGAGCTTAAGA-CA-C-A--AA-G-C-GG-CC-C-A-C-G-TCA-A--G--TA-CC----C--C-GAT-T-CAA--G-GC-A-AT-A--AA-CA--AA-GT-GC-T-A--CGCCCG-CC-GAAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAGAAAA-AACCC-CC-ACG-TGG-AC-C-GGG-G--C-T--A-C----A-CA-C-CCT-AGA-A-CCA-AGAC-CC-ACAGATCAAAGCA-ACAGA-ACTTCTGA-C [...]
+Triacanthodes TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCACGACGAGGGCTTAGCTGTCT-CCTCATTC-AAGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAACCATAAGACGAGAAGACCCTATGGAGCTTTAGA-CACC-A--GA-G-T-AG-AT-C-A-T-G-TTA-AACA--AC-CC-T-TAATT-AA----A-G----GA-CTA--A--AC-CA-AAT--G-C--C-T--A-CT-A-CC-CCCATGTCTTTGGTTGGGGCGACCGCGGGGA-AACACAA-AACCC-CC-GTG-TGG-AA-C-GGG-A--A-C--A-C--CCC-C--T-CCT-ACA-G-CTA-AGAG-TC-TCCACTCTAACGC-ACAGA-ATATCTGA-C [...]
+Gasterosteus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTATTACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CACT-A--AA-G-T-GG-AT-C-A-T-G-TCA-AT-G--AC-CC-T-AAA-T-AA----A-G----GA-TTG--A--AC-AA-GAT--G-G--A-A--C-CC-A-CC-CTGATGTCTTTGGTTGGGGCGACCGCGGGGA-AATAAAT-AACCC-CC-ATG-TGG-AA-T-GGG-A--G-C--A-C--C-C-C--T-CCT-ACA-G-CTG-AGAG-TT-ACAACTCTAATAA-ACAGA-ATTTCTGA-C [...]
+Morone TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATCTTAACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATAACGAGGGCTTAACTGTCT-CCTTTCTC-AAGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTAACACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA-T-A--AG-A-T-AG-AT-T-A-C-C-TTA-ATCA--AC-CC-A-GAA-C-AA----A-G----GG-CGG--A--AC-CA-GAG--G-T--A-A--A-CC-T-TT-CCAACGTCTTTGGTTGGGGCGACCGTGGGGT-AAAACAA-AACCC-CC-ATG-TGG-AA-T-AGG-A--G-C--A-C--C-T-C--T-CCT-TCA-A-CCT-AGAG-CT-CCCGCTCTAAGGA-ACAGA-ATTTCTGA-C [...]
+Capros TAAGAGGTCCCGCCTGCCCTGTGAC-TG-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCTTTTTC-AAGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATACTTACATAAGACGAGAAGACCCTATGAAGCTTTAGA-CACC-A--AA-G-C-AG-CT-C-A-A-G-TTA-AACA--CC-CC-C-TCA-T-AA----G-G----GA-CTA--A--AC-CA-TGT--G-A--A-T--C-CT-G-CC-CTAATGTCTTTGGTTGGGGCGACCGCGGGG--GATAAAA-AGCCC-CC-ATG-TGG-AA-T-GAG-A--T-T--A----ATT-C--T-CTT-AAA-A-CTA-AGAG--CTACCGCTCTAAGAA-ACAGA-ACTTCTGA-C [...]
+Beryx TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CTTTTCTCCAAGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATACAAACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA-C-A--AA-G-C-AG-CC-C-A---A-ATT-A--A--GA-CT-C--CA-A-AA-TTAAAACGG-AG-C----A--AT-AA--AA--T-G--A-CAAC-CCTG-CT-CAAATGTCTTTGGTTGGGGCGACCATGGGGA-AAAACGA-AACCC-CC-ACG-TGG-AA-C-GGA-A--G-A--A-C----TTC--T-TCT-ACA-A-CCA-AGAG-CC-GCCACTCCAAGTG-ACAGA-ATCTCTGA-C [...]
+Melamphaes TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTCAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCCTGACGAGGGCTTAGCTGTCT-CTTTTCTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTTTCTCATAAGACGAGAAGACCCTATGGAGCTTTAGA-CA-C-A--AA-G-C-AA-CC-C-A---A-ATT-A--C--GA-CC-T--TG-A-AA-CTAAACCAG-GG-C----A--AT-AA--AA--T-G--A-C--C-CCTG-CT-CAACTGTCTTTGGTTGGGGCGACCCTGGGGA-AAAACAA-AACCC-CC-ACG-TGG-AA-C-AGA-A--G-A--A-C----CCC--T-TCT-ACA-A-CCA-AGAG-CC-CCTGCTCTAAGTA-ACAGA-ACCTCTGA-C [...]
+Rondeletia TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACAACGAGGGCTTAGCTGTCT-CCTTTTTCT-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATTATAACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CA-C-A--AA-G-C-AG-TC-C-A-C-A-CCA-A--A--CA-CC-C--CA-A-AA--T-AAA-GG-GG-C-A--A--AT-CA--AG--TGG--T-C--C-CCTG-CT-CAAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAAATAA-AACCC-CC-ACG-TGG-AA-T-GAG-A--G-A--A-C----CTC--T-CCC-ACA-A-CCA-AGAG-CC-GCCACTCTAAGTA-ACAGA-ACCTCTGA-C [...]
+Sargocentron TAAGAGGTCCCGCCTGCCCCGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCCTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTAATCTCCCCGTGCAGAAGCGGGGATAAAACCATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CA---A--AA-GAC-GG-AC-C-T-T-G-CAA-A--A--CA-AC-C--CT-G-AA--C-AAA--G-GA-C-A--A--AA-CACCAA--AGG--A-C--T-CC-G-CC-CAAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAAATAA-AACCC-CC-ACG-TGG-AA-T-GGG-A--G-A--A-C----ATC--C-CCC-AAA-A-CTA-AGAG-GT-ACCCCTCTAAGAA-GCAGA-ATATCTGA-C [...]
+Xenolepidichthys TAAGAGGTCCCGCCTGCCCTGTGAC--T-T-TA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCG-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATGCAAATATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--GT-G-C-AG-AT-C-A-C---GAA-A--A--AT-ACTT--T--A-TA-----CA--AAAAGATTA-A--GC-CC--AA--T-G--A-C--T-CCCGCA--TGACTGTCTTTGGTTGGGGCGACCACGGGGA-AAAATAA-AACCC-CC-ACG-AGG-AC-TGAG--AGTT-T------T--A-C--T-CCT-AAA-A-CCA-AGAG-CT-ACAGCTCTAAGTA-TCAGA-AATTCTGA-C [...]
+Allocyttus TAAGAGGTCCCGCCTGCCCTGTGAC--T-T-WA-GTTTAACGGCCGCGGTATYTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAATAACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CC-T-A--GT-G-C-AG-AT-C-A-C---GAA-A--A--AT-ACTT--TA-A-GA----CAA--AAAAGA-AA-A--GC-CC--AA--T-G--A-C--C-CCTGCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ACG-AGG-AC-TGAG--AGTT-T------T--A-C--T-CCT-AAA-A-CCA-AGAG-CC-ACAGCTCTAAGTA-TCAGA-AATTCTGA-C [...]
+Zenopsis TAAGAGGTCCCGCCTGCCCTGTGAC--T-TAAA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATGATAATATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--GT-G-A-AG-AC-C-A-C---GAA-A--A--AA-GCTT--TG-AGTT-----AA--AAAAGA-AA-A--CC-CC--AG--T-G--A-T--T-TCTCCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ACG-AGG-AT-TGAG--AGTT-C------A--A-C--T-CCT-AAA-A-CCA-AGAG-CT-ACAGCTCTAAGAA-ACAGA-AATTCTGA-C [...]
+Zeus TAAGAGGTCCCGCCTGCCCTGTGAC--T-TAAA-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAATAATATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--AT-G-C-AG-TC-C-A-C---GAATA--A--TA-CTTT--TG-A-TG-----AA--GAAAGA-AA-A--GC-TC--AA--T-G--G-C--T-CCTGCA--CGCCTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ATG-AGG-AT-TGAG--AGTT-C------T--A-C--T-CCT-AAA-A-CCA-AGAG-CC-ACAGCTCTAAGTA-ACAGA-AATTCTGA-C [...]
+Zenion TAAGAGGTCCCGCCTGCCCTGTGAC-TT-T-AA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGGAGACCCGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCT-AGTCAATGAAATTGATATCCCCGTGCAGAAGCGGGGATATTCACATAAGACGAGAAGACCCTATGGAGCTTTAGA-CC-T-A--GT-G-C-AG-CC-C-A-C---GAA-A--A--AT-ACTT--TT-A-CA----CAA--GAAAGA-AA-A--GC-CC--AA--T-G--G-C--C-CCCGCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGAA-AAAACAA-AACCC-CC-ACG-AGG-AG-T-GGA-AGCA-C--A---A--G-C--C-ACC-CAA-G-CCA-AGAG-CC-ACAGCTCTAAGCA-TCAGA-AATTCTGA-C [...]
+Parazen TAAGAGGTCCCGCCTGCCCTGTGAC-TT-T-AA-GTTTAACGGCCGCGGTATCTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCACCACGAGGGCTTAGCTGTCT-CCTTTTTCA-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--GT-G-C-AG-CC-C-A-C----AA-A--A--AT-GCTT--TA-A-AA----CAA--AAAA-C-AA-A---C-CC--AA--C-G--A-G--C-CCTGCA--CAACTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ACG-AGG-AC-T-AGA-AGTT-T--A---T--A-C--T-CCT-ATA-A-CCA-AGAG-CC-ACGGCTCTAAGTC-TCAGA-AATTCTGA-C [...]
+Cyttopsis TAAGAGGTCCAGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGAATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAGGACCCGTATGAATGGCTCCACGAGGGCTTAACTGTCT-CCTTTTTCA-GGTCGATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAATTACATAAGACGAGAAGACCCTGTGGAGCTTAAGA-CC-C-A--AT-G-C-AG-GA-C-ACC---TAC-T--A--AC-AC-T--TT-A-GA----CAA--TAAAGACTG-A--GA-CA--TA--T-G--A-C--C-CCTGCA--AGACGGTCTTTGGTTGGGGTGACCGAGGGGA-AAAACAA-AGCCC-CC-ACG-AGG-AC-T-AGG-AG-T-C--T---T--A-C--T--CT-AAA-A-CCA-AGAG-CC-ACAACTCTAAGTA-TCAGA-AATTCTGA-C [...]
+Hoplostethus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACGACGAGGGCCTAGCTGTCT-CCTTTTTCA-GGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATAATCACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CA-C-A--AG-G-C-AG-CC-C-A-C-G-TTA-A--T--AA-CT-T--TC-A-AA--C-AAG--A-AA-CAA--A--AC-TA--AG--TGG--C-G--C-CCTG-CC-AGAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACAA-AACCC-CC-ATG-TGGAAA-A-GGA-G--G-AC-A------C-C--T-CCT-ACA-A-CCC-AGAG-CC-ACTGCTCGAAGTA-ACAGA-ACTTCTGA-C [...]
+Diretmus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-A-TT-GTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCCGTATGAACGGCACGACGAAGGCCCAGCTGTCT-CCTTTTTCA-GGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATGTTAACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CC-C-A--AG-G-C-AG-CC-C-A-C-G-TCA-A--G--CA-CC-C--CC-C-GA--C-AAA--G-GG-TTA--A--AC-CA--AG--TGA--A-G--C-TCTG-CC-CCAGTGTCTTTGGTTGGGGCGACCGCGGGGA-AAAACTA-AACCC-CC-ATG-TAGATA-A-GGA-A--T-A--G-C----C-C--T-CCT-ACA-A-CCA-AGAG-TC-ACCACTCTAAGCA-ACAGA-AATTCTGA-C [...]
+Polymixia_japonica TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCTTAACTGTCT-CCCCTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTGAAA-CC-T----AT-GAT-AG-TA-C-A-C-G-TCA-A--A--CA-CC-T--CA-A-CA--T-AAA--G-AA-A-AG-A--AC-TA--AG--T-G--T-C-TC-CCTA-TC-AAAGTGTTTTTGGTTGGGGCGACCGC-GGGG-AAAACAA-AACCC-CC-ATG-TGG-AC-C-GGG-A--A-T--A-C-TA-A-T--T-CCT-ACA-A-CCCTAGAG-CT-ACCGCTCTAAGTA-ACAGA-ATATCTGA-C [...]
+Polymixia_lowei TAAGAGGTCCCGCCTGCCCTGTGAC-TC-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATAACGAGGGCTTAACTGTCT-CCCCTTTCT-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTGAAA-CC-T----AT-GAT-AG-TG-C-A-C-G-TCA-A--A--CA-CC-T--CA-G-CA--C-AAA--G-AA-A-AG-A--AC-TA--AG--T-G--T-T-TA-CCTA-TC-AAAGTGTTTTTGGTTGGGGCGACCGC-GGGG-AAAACAA-AACCC-CC-ATG-TGG-AC-C-GGG-A--A-T--A-C-TA-A-T--T-CCT-ACA-A-CCCTAGAG-CT-ACCGCTCTAAGTA-ACAGA-ACATCTGA-C [...]
+Percopsis_omiscomaycus TAAGAGGTCCCGCCTGCCCTGTGAC--A-A-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAACACATAAGACGAGAAGACCCTATGGAGCTTAAGA-CC-A-A--CC-T-C-GG-CC-C-A-T-G-TGG-A--G--C--AC-T--CA-A-C-----AAA--G-G--C-AG-A--AC-TA--AG--TGG--A----C-CCGA-G--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGG-ATCAACA-AGCCC-CC-ATG-TGG-AA-T-A-G-AG-A-A--A-CAT----C--T--CT-AGA-A-CCT-AGAG-CT-ACTGCTCCAAGTA-ACAGA-ACATCTGA-C [...]
+Percopsis_transmontana TGAGAGGTCCCGCCTGCCCTGTGAC--A-A-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAAAGGCATCACGAGGGCTTAGCTGTCT-CCTTTTTCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATGCGCACATAAGACGAGAAGACCCTATGGAGCTTAAGA-CC-T-C--CC-C-C-GA-CC-C-A-T-G-TGA-C--A--C--AC-T--CA-A-C-----AAA--G-G--C-AG-A--AC-TT--AA--TGG--A-C--C-CCGG-G--AAACTGTCTTTGGTTGGGGCGACCGCGGGGG-ATGA-AA-AGCCC-CC-ATG-TGG-AA-T-A-G-AG-A-A--A-CAT----C--T--CT-AAA-A-CCC-AGAG-CC-ACTACTCCAAGTA-ACAGA-ACATCTGA-C [...]
+Forbesichthys TAAGAGGTCCCGCCTGCCCTGTGAC--A-T-CTAGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCATAACTGTCT-CCTCTCTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATATAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--CTC-C--CCTC-T-AA-CT-T-G-T-G-CAA-A--AG-CT-CC-T--CA-A-CA----ACA--G-GA-C-CA-A--AC-T---AA--T-A--A-G--C-CATA-G--AGACTGTCTTTGGTTGGGGCGACCTTGGGGA-ATAA-AA-AACCC-CC-ATG-CGG-AA-T-A-G--G-AGT--A-C-C----C--T-CCT-TAA-A-CCC-AGAG-CC-ACCCCTCGAAGTA-ACAAA-ACATTTGA-C [...]
+Speoplatyrhinus TAAGAGGTCCCGCCTGCCCTGTGAC--A-C-CTGGTTTAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCTTAACTGTCT-CCTTTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGAGGATATAAACATAAGACGAGAAGACCCTGTGGAGCTTAAGA--C-T-C--CCTC-T-AA-CT-T-A-T-G-CAA-A--A--CT-CC-T--CA-A-TA----ACA--G-GA-C-CA-A--GC-T---AA--T-A--A-G--C-CACA-G--AAGCTGTCTTTGGTTGGGGCGACCCCGGGGA-ATAA-AA-AGCCC-CC-GTG-CGG-AA-T-A-A--G-AGT--A-T-T----C--T-CTT-TAA-A-CCC-AGAA-CC-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Amblyopsis TAAGAGGTCCCGCCTGCCCTGTGAC--A-C-CTAGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCTTAGCTGTCT-CCTCTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATATAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--C-C-C--CCTC-T-AA-CT-T-A-T-G-CAAGA--AG-CC-CC-T--CA-A-CA----ACA--G-GA-C-CA-A--GC-T---AA--T-A--A-G--G-CATA-G--AGCCTGTCTTTGGTTGGGGCGACCCTGGGGA-ATAA-AA-AACCC-CC-ATG-CGG-AA-C-A-G--G-ACT--C-C-C----C--T-CCT-TAA-A-CCC-AGAG-CG-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Typhlichthys TAGGAGGTCCTGCCTGCCCTGTGAC--A-C-CCAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAAGGCTTAACTGTCT-CCTCTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--C-T-C--CCTC-T-GA-CT-T-A-T-G-CAA-C--A--CC-CC-T--TA-A-TA----ACA--G-GA-C-CA-A--GC-T---AG--T-A--A-G--C-TACA-G--AAACTGTCTTTGGTTGGGGCGACCCCGGGGA-ACAA-AA-ACCCC-CC-ATG-AGG-AA-T-A-A--G-AGT--A-C-T----C--T-CCT-TAA-A-CCC-AGAG-CC-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Chologaster TAAGAGGTCCTGCCTGCCCTGTGAC--A-C-CTAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCAACACGAGGGCTAAACTGTCT-CCTTTTTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATATAAACATAAGACGAGAAGACCCTGTGGAGCTTAAGA--C-T-A--CCTC-T-AA-CT-T-A-T-G-CAA-A--A--CT-CC-T--CA-A-CA----ACA--G-GA-C-TA-A--CT-T---AA--T-A--A-A--C-TATA-G--AAATTGTCTTTGGTTGGGGCGACCCCGGGGA-ACAA-AA-AACCC-CC-GTG-CAG-AA-T-A-G--G-TAC--A-C-C----C--T-CCT-TAA-A-CCC-AGAG-CC-ACCCCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Aphredoderus TAAGAGGTCCCGCCTGCCCTGTGAC--A-T-CTAGTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCACTTGTCTCTTAAATAGAGACCTGTATGAATGGCAACACGAGGGCTTAACTGTCT-CCTTTCTCC-AGTCAGTGAAATTGATCCCCCCGTGCAGAAGCGGGGATAAAAACATAAGACGAGAAGACCCTATGGAGCTTAAGA--C-A-C--CC-A-T-AA-CT-T-A-T-GCGAA-A--A--TT-CT-T--AA-ATCA----AAA--A-GA-A-AG-A--GC-TA--AA--T-A--A-G--C-CTTA-G--TAAATGTCTTTGGTTGGGGCGACCACGGGGG-ATAATAA-AGCCC-CC-ATG-CGG-AA-T-A-G--G-A-C--A---T----C--T-CCT-TAA-C-CTC-AGAG-CC-ACCGCTCTAAGTA-ACAAA-ACATTTGA-C [...]
+Coelorinchus TAAGAGGTCTCGCCTGCCCAGTGAC-TAAA-T--GTTTAACGGCCGTGGTATCTTAACCATGCGAAGGTAGCGTAATCATTTGTCTTTTAAATGAAGACCCGTATGAATGGCAAAACGAGGGCTTAACTGTCT-CCCCTCCCC-AGTCAATGAAATTGATCTCCCCGTGCAGAAGCGAGGATAAAATTATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CT-T-A--AA-A-TAA-CCC-T-G-T---AAA-A--T--AA-AC-T-TTG-A-TA----CAA--A-CA-C-AA-A---C-TT--AA----G--G-A--GTTTTATT--TAAATGTCTTTGGTTGGGGTGACCACGGGGT-AAAACAT-AACCC-CC-ACG-AAG-AT---TGG-GA-A-C--A---T--A-C--T-CCT-AAC-A-CCA-AGAG-AC-ACCCCTCTAAGCA-ACAAA-ATTTTTGA-C [...]
+Bregmaceros TGAGAGGTCCCGCCTGCCCAGTGAC-TA-T-AT-GTTAAACGGCCGTGGTATCTTAACCATGCTAAGGTAGCGAAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCCCCACGAGGGCTTGACTGTCT-CCTTCCCCC-AGTCAATGAAATTAAACTTCCCGTGCAGATGCGGGAATAAGCGCATAAGACGAGAAGACCCTTTGGAGCTTCAGA-CC-C-T--AA-A-TAAGTTA-T-G-T---TAA-A--C--AC-CC-T--T--C-AC----CGA--G-TA-A-AA-A---C-AT--AG--T-A--G-T----TTTATT--CAAGGGTCTTAGGTTGGGGCGACCACGGAGT-AAAATA--AACCCTCC-ACG-AAG-A----AGG-GG-C-C--T-C-TATAAG--C-CCT-AAA-T-CCC-CGAT-AA-TCACATCTAAGAA-ACAGA-ATTTCTGA-C [...]
+Stylephorus TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AA-GTTTAACGGCCGTTTTATCTTAACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCCCCCTCC-AGTCAATGAAACTGACCTCCCCGTGCAGAGGCGGGGATTATTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-G-TAGTGCA-T-G-T---CTA-A--A--AT-AC-T-AGA-A-AA----TAA--G-AA-A-AA-A---C-CC--AA--T-G--C-C--C-CCTACT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAA-AACCC-CC-ATG-TAG-AC---CGG-GG-A-A--A-C----A-T--C-CCT-AAA-A-CCC-AGAG-CA-ACCACTCTAAGAA-ACAAA-ACCTTTGA-C [...]
+Urophycis TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-A-TGTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCCCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATTAAAACATAAGACGAGAAGACCCTGTGGAGCTTAAGA-CC-T-A--AT-A-TAATTTA-T-G-T---ATA-A--T--AC-AC-T-AAA-A-TA----ACA--G-CT-A-AA-A---C-TC--AA--T-A--G-T--A-ATTATA--GAGGTGTCTTTGGTTGGGGCGACCGCGGGGT-ACAACAA-AACCC-CC-GCG-TGG-AT---TGG-GAGA----A-C-T----T--CTCCT-AGC-A-CCC-AGAG-CC-GCTACTCCAAGTA-ACAGA-ATTTCTGACT [...]
+Steindachneria TGAGAGGTCCAGCCTGCCCTGTGAC--A-T-A--GTTTAACGGCTGCGGTATTTTGACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGGAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTCC-AGTCAATGAACTTGACCTCCCCGTGCAGAGGCGGGGATTAGTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-TC-T-A--GA-A-TAAACCA-T-G-T---AAA-A--C--AA-GC-T-GTA-A-TA----CCA--G-CA-T-AA-A---C-CA--AT--T-G--G-T--A-CCTATT--CAAATGTCTTTGGTTGGGGCAACCGCGGAGA-AAAATTT-AACCT-CC-ATG-TGG-AC---CGG-GG-G-T--A-C-T--A-C--C-CCT-AGA-A-CTC-AGAA-CC-ACCATTCCAAGAA-ACAGA-ACTTCTGACC [...]
+Macruronus TRRGAGGTCTCGCCTGCCCTGTGAC-TATT-A--GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGTGGACCTGTATGAACGGCATCACGAGGGCTTAACTGTCT-CCCCTCTCC-AGTCAATGAAATTAACCTCCCCGTGCAGAGGCGGGGATAAGAATATAAGACGAGAAGACCCTGTGGAGCTTTAAA-CC-T-A--AG-A-CAAACCA-T-T-C---CTA-G--T--AA-GC-T-GTG-A-TA----CCA--G-TATT-AAGA---C--T--AG--T-G--G-T--T-TTTGTT--GAAGTGTTTTTGGTTGGGGTGACCATGGGGA-AAAACAC-AACCC-CC-ACG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAC-A-CTG-AGAG-CC-CACACTCCAAGTA-ACAGA-ACTTCTGACC [...]
+Bathygadus TAAGAGGTCTCGCCTGCCCGGTGAC-TATA-T--GTTTAACGGCCGCGGTATTTTAACCGCGCGAAGGTAGCGTAATCATTTGTCTTTTAAATGAAGACCTGTATGAATGGTATTACGAGGGCTCAACTGTCT-CCCTTCTCC-AGTCAATGAAATTGACTTCCCCGTGCAGAGGCGGGGATATTAATATAAGACGAGAAGACCCTGTGGAGCTTAAGA-CC-T-A--AG-A-TAAGCCA-T-G-T---TCA-G--G--AA-TC-TAAAA-A-CA----TAA--G-TA-T-AA-A---C-TT--AG--T-G--G-C--A-TTTATT--GAAGTGTCTTCGGTTGGGGTGACCCTGGGGA-AAAACTT-AACCC-CC-AAG-TAG-AC---TGG-GT-A-C--A-T-T--G-T--C-TCT-AGA-A-CTC-AGAG-CC-CATACTCCAAGTA-ACAGA-ATATTTGA-C [...]
+Muraenolepis TAGGAGGTCCCGCCTGCCCTGTGAC-TAAT-A--GTTTAACGGCCGCGGTATTTTAACCGTGCAAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCTTTTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAAGCACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAGCTA-C-G-T---TTA-A--C--AG-CC-T-GTA-A-AA----TCA--G-AA-A-TA-A---C-TT--AG--T-A--G-T--C-TTTATT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-C-T--A-T--C-CCT-AAT-A-CCA-AGGG-CC-TCCCCCCCAAGTA-ACAGA-ACTTCTGACC [...]
+Physiculus TAAGAGGTCCCGCCTGCCCTGTGAC-GAAA----GTTTAACGGCCGCGGTATTCTAACCGTGCGAAGGTAGCGTAATCACTTGTTTTTTAAATGGAGACCAGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCTTCTTT-AGTCAATGAAATTGACCTTCCCGTGCAGAGGCGGGAATTACTATATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAGTCA-C-A-T---TTA-A--C--AT-GC-T-TAA-A-CA----ACA--G-TA-A-AA-A---T-AT--AG--T-G--A-A--ACATTATT--GAAGTGTCTTTGGTTGGGGCGACCATGGGGT-AAAACAC-AACCC-CC-ATA-CGG-AC---TGG-GG-A-T--A-C-A--A-T--C-CCT-AAT-A-CCC-AGAG-CC-TCCGCTCCAAGTA-ACAGA-ATTTCTGA-C [...]
+Merluccius TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATCTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCTCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATATTTATATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-G-TAAACCA-C-G-T---TTA-A--T--GT-AC-T-AGA-ATTA----ATA--G-CA-A-AA-A---C-TT--AG--TGG--A-C--A-TTTATT--TAAGTGTCTTTGGTTGGGGCGACCGCGGAGT-AAAACAT-AACCT-CC-ATG-TGG-A----CGG-GG-A-T--A-C-T--T-T--C-CCT-AAA-A-CTC-AGAG-CC-TCCACTCCAAGCA-ACAGA-AATTCTGACC [...]
+Melanonus TAAGAGGTCCCGCCTGCCCACTGAC-TA-T-AT-GTTCAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAACTGTCT-CCCCCCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATACCCCTATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAATTA-T-G-T---TCA-A--C--AC-TC-T-ACA-A-AA----CCA--G-TA-A-AA-A---C-TT--AA--T-A--A-C--A-TTTATT--CAAGTGTCTTTGGTTGGGGCGACCGAGGGGA-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAC-A-CTC-AGAG-CC-GCTACTCCAAGTA-ACAGA-AATTCTGACC [...]
+Raniceps TAAGAGGTCCCGCCTGCCCTGTGAC-TT-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCCCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATATTTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-G-TAAGCCA-T-G-T---TTA-G--T--AT-CC-T-GAG-A-TA----TCA--G-TA-A-AA-A---C-TT--AA--T-G--G-C--A-ATTATT--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAC-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T--A-T-T--A-T--C-CCT-AAT-A-CTC-AGAG-CC-GCTACTCCAAGTA-ACAGA-AATTCTGAC- [...]
+Trachyrincus TAAGAGGTCCCGCCTGCCCAGTGAC-TACA-T--GTTTAACGGCCGCAGTATTTTAACCGCGCGAAGGTAGCGTAATCACCTGTTTTTTAAATGAAGACCTGTATGAATGGCTCAACGAGGGCTTAACTGTCT-CCCTCCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATATTTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T-A--AA-A-TAAGTCA-C-G-T---TTA-A--C--AT-TC-T-GTA-A-TA----TCA--G-TA-A-AA-A---C-TC--AG----C--G-A--CGATTATT--GAAGTGTCTTCGGTTGGGGCGACCCTGGGGA-AAAACAC-AACCC-CC-ATG-TGG-AC---TGG-GA-A-T--A-C-T--A-T--T-CCT-AAC-A-CTC-AGAG-CC-TCTACTCCAAGTA-ACAGA-AATTCTGA-C [...]
+Euclichthys TAAGAGGTCCCGCCTGCCCAGTGAC-TA-T-AA-GTTTAACGGCCGCGGTATTTTAACCGTGCGAAGGTAGCGTAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATCACGAGGGCTTAGCTGTCT-CCCCTCTCC-AGTCAATGAAATTGACCTCCCCGTGCAGAGGCGGGGATAAATATATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CC-T----AA-G-TAAATCA-C-G-T---TTA-A--C--AT-CC-T-AGA-A-CA----ATA--G-AA-T-AA-A---C-CT--AG--T-G--A-A--A-ATTATG--GAAGTGTCTTTGGTTGGGGCGACCGCGGGGT-AAAACAA-AACCC-CC-ATG-TGG-AC---CGG-GG-A-T----G-T--A-T--C-CCT-AAC-A-CTC-AGAG-CC-TATACTCCAAGTA-ACAGA-AAATCTGACC [...]
+Synodus TAAGAGGTCCCGCCTGCCCTGTGAC-T--A-AT-GTTTAACGGCCGCGGTATCTTGACCGTGCGAAGGTAGCGCAATCACTTGTCCTTTAAATGGGGACCTGTATGAATGGCACAACGAGGGCTTAACTGTCT-CCCCCCTCC-TGTCAGTGAAACTGATCTCCCCGTGAAGAAGCGGGGATTCCACTACCAGACGAGAAGACCCTATGGAGCTTAAAA-CA---A--AA-G-A-GG-GC-C---T---ATA-T--A--AA-CC-A--A--G-GG--C-AGA--T-AA-A-C--AC-AG-CAGTTGTTTAG--T-T--C-CCT--CC-GTAGT-T-TTTGGTTGGGGCGACCGTGGAGA-AACAAAA-AACCC-CC-ATG-CAG-AA-C-AGG-A--T-T--A-C---TAGAA-C-CTT-A-A-A-CCC-AGAG-CC-ACAGCTCTAAGTA-TCAAA-ATATTTGA-- [...]
+Chlorophthalmus TAAGAGGTCCCGCCTGCCCAGTGACTTG-T-ATAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCCTTTAAATGGGGACCTGTATGAATGGCACGACGAGGGCTTAGCTGTCT-CCCCTATCC-TGTTAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATAACTACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CA---CTTAA-G-C-GA-CC-C-A-A---ATA-G--AGCAA-AC-T-CA--C-CA--C-AAA--T-GA-GCTG-AC-TC-CCGATG-GTAA--G-A--C-AC---CGTTTAGTGTCTTTGGTTGGGGCGACCGTGGGGA-AAAGAAA-AACCC-CC-ATG-AGG-AC-CTGGG-G--C-G--ACC---C--CC-C-CCC-ATA-G-CCG-AGAGCCC-ACCACTCGAAGCA-TCAGA-ACCTCTGA-C [...]
+Macroparalepis TAAGAGGTCCCGCCTGCCCTGTGACCCC-C-AAAGTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCCTTTAAATGAGGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCCCTGTCC-AGTCAGTGAAATTGATCTCCCCGTGCAGAAGCTGGGATAAAACCATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CG---ATTAG-A-T-GA-CC-C-G-C---ATG-A--GGCCG--C-T--T--C-AA--C-ACA--A-TT-GGGG--CGAC-CCCTCA-GTGATTT-A--T-CCT--CATCCTATGTCTTTGGTTGGGGCGACCGTGGGGG-AAAGAAT-ATCCC-CC-ATGTAGG-AC-TGAAA-A--C-C--A-C---T--CC-T-TTT-ATA-G-CTA-AGAGCCT-ACCACTCGAAGCA-TCAGA-ATTTCTGA-C [...]
+Diaphus TAAGSGGTCCCGCCTGCCCWGTGAC-CA-T-GT-GTTCAACGGCCGCGGTATTCTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAAAGGCATCACGAGGGCTTGACTGTCT-CCCCTTTAA-GGTCAATGAAATTGATCTCCCCGTGCAGAAGCGGGGATACGCTCGTAAGACGAGAAGACCCTATGGAGCTTAAGA-CA-T-A--AG-G-C-GA-CC-C-A-C-G-TCA-A--A--AACCC-TCCC--C-CCT-TAAGA--G-GA-A-AT-G--AA-CA--AA-GT-G--G-G--C-CTCA-CC-GAAATGTCTTCGGTTGGGGCGACCGCGGGGA-AAGACCA-AACCC-CC-ACA-TGG-AT-T-AAG-A--C-C--ACA----A-TAGC-CTT-AAA-A-CCC-AGAC-CT-CCAAGTCAAATCA-ACAGA-ATTTCTGA-C [...]
+Monocentris TAAGAGGTCCCGCCTGCCCTGTGAC-TA-T-AT-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCCGTATGAATGGCACGACGAGGGCCTAACTGTCT-CCTTTTTCA-GGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATAACTACATAAGACGAGAAGACCCTATGGAGCTTCAGA-CA-C-A--AA-G-C-AG-CC-C-A-C-G-TTA-A--G--AA-AC-C--CC-A-AA--C-AAG--G-AA-CTA--A--AC-TA--AG--TGA--C-G--C-CCTG-CC-AGAATGTCTTTGGTTGGGGCGACCGCGGGGA-AAGACTA-AACCC-CC-ATG-TGGAAA-G-GGA-A--G-ACTA-C----C-C--T-CCT-ACA-G-CCA-AGAG-CC-ACTGCTCTAAGTA-ACAGA-ATTTCTGA-C [...]
+Brosmophycis TAAGAGGTCCCGCCTGCCCTGTGAC-AA-T-AC-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTCTTAAATGGAGACCTGTATGAATGGCACAACGAGGGCTTAACTGTCT-CCTTTCCCT-AGTCAATGAAATTGATCTTCCCGTGCAGAAGCGGGAATTAATACATAAGACGAGAAGACCCTATGGAGCTTTAGA-TACT-A--AA-A-C-AG-CC-C-A-T-G-TTA-A--A--GA-CC-C--CA-T-AA--T-AAA--G-GAGC-A--A--AC-TA--AA--T-G--G-C--C-CCTG-TC-CTAATATCTTTGGTTGGGGCGACCGCGGGGA-AATATTA-AACCC-CC-ATG-TGG-AA-T-GGG-A--G-C--A------C-C--T-CCC-CCAGAGCCA-AGAG-CA-ACAGCTCTAAGCA-ACAGA-ACATCTGA-C [...]
+Opsanus TAAGAAGTCCCGCCTGCCCCGTGAC--A-C-AA-GTTTAACGGCTGCAGTAATATAACTGTACAAAGGTAGCGTAATCACCTGTCTTTTAATTGAAGACCTGTATGAATGGCATCACGAGGATTTAACTGTCTCTACTTTTC--AATCAATGAAATTGTTTTTCCCGTGCAAAAACGGGAATATATCTATAAGACGAGAAGACCCTGTGGAGCTTTA-A--G-T-A--AC-C-C-AG----------G-----A--A--TG-TA-T--TA---AA----ACA----TA-C-A--T--TT-TA--CC--T-A--A-A--A-------C-TTAC--T-TTTGGTTGGGGCGACCATGAAGA-AAAAAAG-AACCT-TC-ATA-AGG-AA-C-GGA-A--G----A--------C--T-CCT-AAA-A-C-A-CGAA-CG-ACAGTTCTAATTA-ACAGA-ATTTCTGA-C [...]
+Chaunax TAAGAGGTCCCGCCTGCCCAGTGAC-TA-C-AA-GTTCAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGTAATCATTTGTCTTTTAAATTAAGACCTGTATGAAAGGTGAGACGAGGGCTTAGCTGTCT-CCTCTCTC-CAGTCAATGAAATTGATCCCCCCGTGCAGAAGCGGGGATTTTAACATAAGACGAGAAGACCCTGTGGAGCTTTAGA-CACT-C--GG-G-C-AG-AC-T-A-T-G--TC-AAGT--AC-CC-C-TAA-T-AA----A-G----GT-GAA--A--ACAGAGTAT--G----C-T--A-CT-G-TC-CCAATGTCTTCGGTTGGGGCGACCATGGGGA-AATAAGA-AACCC-CCAAAG-TGG-AA-T-GGA-A--A-CAGA-CC-CTT-T--T-TCT-ACA-A-CTG-AGAG-TA-CCCCCTCTAGCTA-ACAGA-ACTTCTGA-C [...]
+Lycodes TAAGAGGTTCCGCCTGCCCTGTGAC-TA-T-TA-GTTTAACGGCCGCGGTATTTTGACCGTGCGAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCATAACGAGGGCTTAGCTGTCT-CCTTTTTC-CAGTCAATGAAGTTGATCTTCCCGTGCAGAAGCGGGAATACAAACATAAGACGAGAAGACCCTATGAAGCTTTAGA-CACC-A--AG-A-C-AG-CT-C-A-T-G-TTA-AT-A--AC-CC-T-GAA-T-AA----A-G----GC-TTA--A--AC-CA-AAT--G-A--A-G--C-CT-G-TC-CGAATGTCTTTGGTTGGGGCGACCGCGGGGC-ATTAAAA-AACCC-CC-ACG-TGG-AA-T-GGG-A--G-C--A-C--C-C-C--T-CCT-ACA-A-CTA-AGAG-CC-ACAGCTCTAGTAA-ACAGA-AATTCTGA-C [...]
+Arcos TAGGAGGTCCCGCCTGCCCTGTGAC-TA-T-GG-GTTCAACGGCCGCGGTATTTTGACCGTGCAAAGGTAGCGCAATCACTTGTCTTTTAAATGAAGACCTGTATGAATGGCGAAACGAGGGCTCAACTGTCTCCCCCTTTT--AATCAGTGAAATTGATCTCCCCGTGCAGAAGCGGGGATACCACCATAAGACGAGAAGACCCTGTGGAGCTTTAGA-TA-T-AT-AA-A-G-GG-AT-T-A-TAC-CAA-AT-T--TG-CC-T--TC-T-AA----ACA----GG-CTA--A--AC-TA--AT--T-A--ATA--T-CC-T-TT-TTGCTGTCTTTGGTTGGGGCGACCACGGGGA-AAAATAA-AACCC-CC-ACG-CGG-AT-A-AAA-A--G-A--A-C--C-CGC--T-TTT-ACAGA-GT--AGAG-CC-TCAGCTCT-ACAACACAGA-ACTTCTGA-C [...]
\ No newline at end of file
diff --git a/tests/kmeans/Grande_2013/partition_finder.cfg b/tests/kmeans/Grande_2013/partition_finder.cfg
new file mode 100755
index 0000000..40cf46c
--- /dev/null
+++ b/tests/kmeans/Grande_2013/partition_finder.cfg
@@ -0,0 +1,19 @@
+## ALIGNMENT FILE ##
+alignment = alignment.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G;
+model_selection = AIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+#tiny = 1-2;
+blah = 3-2000;
+
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = kmeans;
diff --git a/tests/kmeans/__init__.py b/tests/kmeans/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/kmeans/fabrications1/README.yaml b/tests/kmeans/fabrications1/README.yaml
new file mode 100755
index 0000000..8de602c
--- /dev/null
+++ b/tests/kmeans/fabrications1/README.yaml
@@ -0,0 +1,23 @@
+study:
+ reference: "Grande T, Borden WC, Smith WL (2013) Limits and relationships of Paracanthopterygii: A molecular framework for evaluating past morphological hypotheses. Mesozoic Fishes 5: 385-418. ISBN:978-3-89937-159-8"
+ DOI: NA
+
+dataset:
+ DOI: dx.doi.org/10.5061/dryad.k4m8t
+ license:
+ type: CC0
+ notes: ""
+ mitochondrial: yes
+ nuclear: yes
+ chloroplast: no
+ datatype: dna
+ number of taxa: 65
+ number of sites: 4027
+ number of data blocks: 12
+ used for tree inference: yes
+ study clade:
+ latin: "Paracanthopterygii"
+ english: "paracanthopterygian fish"
+ notes: ""
+
+notes: "The ms does not have a DOI, but it has an ISBN: ISBN:978-3-89937-159-8. The data blocks in this dataset were inferred with reference to the readme text associated with the dataset on dryad. Codon positions in each coding gene may not correspond with each other (i.e. '1' is not necessarily 1st codon position)."
\ No newline at end of file
diff --git a/tests/kmeans/fabrications1/alignment.phy b/tests/kmeans/fabrications1/alignment.phy
new file mode 100755
index 0000000..5b4562c
--- /dev/null
+++ b/tests/kmeans/fabrications1/alignment.phy
@@ -0,0 +1,6 @@
+5 7
+one AAAAAAA
+two ACCCCCC
+three ATTTTTT
+four AAGGGGG
+five AGAAAAA
diff --git a/tests/kmeans/fabrications1/partition_finder.cfg b/tests/kmeans/fabrications1/partition_finder.cfg
new file mode 100755
index 0000000..217b4cc
--- /dev/null
+++ b/tests/kmeans/fabrications1/partition_finder.cfg
@@ -0,0 +1,17 @@
+## ALIGNMENT FILE ##
+alignment = alignment.phy;
+
+## BRANCHLENGTHS ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+models = GTR+G;
+model_selection = AIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+all = 1-7;
+
+## SCHEMES, search: all | user | greedy ##
+[schemes]
+search = kmeans;
diff --git a/tests/kmeans/fabrications2/README.yaml b/tests/kmeans/fabrications2/README.yaml
new file mode 100755
index 0000000..8de602c
--- /dev/null
+++ b/tests/kmeans/fabrications2/README.yaml
@@ -0,0 +1,23 @@
+study:
+ reference: "Grande T, Borden WC, Smith WL (2013) Limits and relationships of Paracanthopterygii: A molecular framework for evaluating past morphological hypotheses. Mesozoic Fishes 5: 385-418. ISBN:978-3-89937-159-8"
+ DOI: NA
+
+dataset:
+ DOI: dx.doi.org/10.5061/dryad.k4m8t
+ license:
+ type: CC0
+ notes: ""
+ mitochondrial: yes
+ nuclear: yes
+ chloroplast: no
+ datatype: dna
+ number of taxa: 65
+ number of sites: 4027
+ number of data blocks: 12
+ used for tree inference: yes
+ study clade:
+ latin: "Paracanthopterygii"
+ english: "paracanthopterygian fish"
+ notes: ""
+
+notes: "The ms does not have a DOI, but it has an ISBN: ISBN:978-3-89937-159-8. The data blocks in this dataset were inferred with reference to the readme text associated with the dataset on dryad. Codon positions in each coding gene may not correspond with each other (i.e. '1' is not necessarily 1st codon position)."
\ No newline at end of file
diff --git a/tests/kmeans/fabrications2/alignment.phy b/tests/kmeans/fabrications2/alignment.phy
new file mode 100644
index 0000000..84082e8
--- /dev/null
+++ b/tests/kmeans/fabrications2/alignment.phy
@@ -0,0 +1,7 @@
+6 3037
+10CH AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATGGAACATTATATTTCATTTTTGGAATTTGAGCAGGATTAGTTGGTACTTCATTAAGACTAATAATCCGAACAGAATTGGGGAAACCTGGTTCACTACTCAATGACGATCAATTATATAACGTAGTAGTAACTGCTCATGGCTTCATTATAATTTTTTTCATAGTTATACCTATTATAATTGGGGGTTTTGGTAATTGATTAGTACCTTTAATACTAGGAGCCCCAGACATAGCTTTTCCACGTATAAATAATATAAGATTTTGACTACTTCCACCATCTCTGACATTATTATTAGCCTCATCAGCAGTCGAAAGAGGGGCTGGTACTGGATGGACAGTTTATCCTCCTTTATCTAGAAACTTATCTCACGCTGGACCCTCAGTAGATTTAGCTATTTTTTCACTTCACTTAGCTGGTATTTC [...]
+12CH AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACATTATATTTCATTTTAAGGAATTGAGCAGGATTAGTTGGTACTTCATTAAGACTAATAATCCGAACAGAATTGGGGAAACCTGGTTCACTACTCAATGACGATCAATTATATAACGTAGTAGTAACTGCTCATGGCTTCATTATAATTTTTTTCATAGTTATACCTATTATAATTGGGGGTTTTGGTAATTGATTAGTACCTTTAATACTAGGAGCCCCAGACATAGCTTTTCCACGTATAAATAATATAAGATTTTGACTACTTCCACCATCTCTGACATTATTATTAGCCTCATCAGCAGTCGAAAGAGGGGCTGGTACTGGATGGACAGTTTATCCTCCTTTATCTAGAAACTTATCTCACGCTGGACCCTCAGTAGATTTAGCTATTTTTTCACTTCACTTAGCTGGTATTTC [...]
+13CH AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGTACTTCATTAAGACTAATAATCCGAACAGAATTGGGGAAACCTGGTTCACTACTCAATGACGATCAATTATATAACGTAGTAGTAACTGCTCATGGCTTCATTATAATTTTTTTCATAGTTATACCTATTATAATTGGGGGTTTTGGTAATTGATTAGTACCTTTAATACTAGGAGCCCCAGACATAGCTTTTCCACGTATAAATAATATAAGATTTTGACTACTTCCACCATCTCTGACATTATTATTAGCCTCATCAGCAGTCGAAAGAGGGGCTGGTACTGGATGGACAGTTTATCCTCCTTTATCTAGAAACTTATCTCACGCTGGACCCTCAGTAGATTTAGCTATTTTTTCACTTCACTTAGCTGGTATTTC [...]
+1CH AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATATTGGAACATTATATTTCATTTTTGGAATTTGAGCAGGATTAGTTGGTACTTCACTAAGACTAATAATCCGAACAGAATTGGGGAAACCTGGTTCACTACTCAATGACGATCAATTATATAACGTAGTAGTAACTGCTCATGGCTTCATTATAATTTTTTTCATAGTTATACCTATTATAATTGGGGGTTTTGGTAATTGATTAGTACCTTTAATACTAGGAGCCCCAGACATAGCTTTTCCACGTATAAATAATATAAGATTTTGACTACTTCCACCATCTCTGACATTATTATTAGCCTCATCAGCAGTCGAAAGAGGGGCTGGTACTGGATGGACAGTTTATCCTCCTTTATCTAGAAACTTATCTCACGCTGGACCCTCAGTAGATTTAGCTATTTTTTCACTTCACTTAGCTGGTATTTC [...]
+4CH AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACATTATATTTCATTTTTGGAATTTGAGCAGGATTAGTTGGTACTTCATTAAGACTAATAATCCGAACAGAATTGGGGAAACCTGGTTCACTACTCAATGACGATCAATTATATAACGTAGTAGTAACTGCTCATGGCTTCATTATAATTTTTTTCATAGTTATACCTATTATAATTGGAGGTTTTGGTAATTGATTAGTACCTTTAATACTAGGAGCCCCAGACATAGCTTTTCCACGTATAAATAATATAAGATTTTGACTACTTCCACCATCTCTGACATTATTATTAGCCTCATCAGCAGTCGAAAGAGGGGCTGGTACTGGATGGACAGTTTATCCTCCTTTATCTAGAAACTTATCTCACGCTGGACCCTCAGTAGATTTAGCTATTTTTTCACTTCACTTAGCTGGTATTTC [...]
+6CH AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGATATTGGAACATTATATTTCATTTTTGGAATTTGAGCAGGATTAGTTGGTACTTCATTAAGACTAATAATCCGAACAGAATTGGGGAAACCTGGTTCACTACTCAATGACGATCAATTATATAACGTAGTAGTAACTGCTCATGGCTTCATTATAATTTTTTTCATAGTTATACCTATTATAATTGGGGGTTTTGGTAATTGATTAGTACCTTTAATACTAGGAGCCCCAGACATAGCTTTTCCACGTATAAATAATATAAGATTTTGACTACTTCCACCATCTCTGACATTATTATTAGCCTCATCAGCAGTCGAAAGAGGGGCTGGTACTGGATGGACAGTTTATCCTCCTTTATCTAGAAACTTATCTCACGCTGGACCCTCAGTAGATTTAGCTATTTTTTCACTTCACTTAGCTGGTATTTC [...]
diff --git a/tests/kmeans/fabrications2/partition_finder.cfg b/tests/kmeans/fabrications2/partition_finder.cfg
new file mode 100644
index 0000000..23f0a2c
--- /dev/null
+++ b/tests/kmeans/fabrications2/partition_finder.cfg
@@ -0,0 +1,22 @@
+## ALIGNMENT FILE ##
+alignment = alignment.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = unlinked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = GTR+G;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+all = 1-3037;
+
+## SCHEMES, search: all | greedy | rcluster | hcluster | user | kmeans ##
+[schemes]
+search = kmeans;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/kmeans/test_kmeans.py b/tests/kmeans/test_kmeans.py
new file mode 100644
index 0000000..6d68119
--- /dev/null
+++ b/tests/kmeans/test_kmeans.py
@@ -0,0 +1,10 @@
+import os
+import pytest
+from partfinder import main, util, analysis, config
+from zipfile import ZipFile
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+def test_grand():
+ full_path = os.path.join(HERE, "Grande_2013")
+ main.call_main("DNA", '--raxml "%s"' % full_path)
diff --git a/tests/misc/Caterino_2001.phy b/tests/misc/Caterino_2001.phy
new file mode 100644
index 0000000..adba7e2
--- /dev/null
+++ b/tests/misc/Caterino_2001.phy
@@ -0,0 +1,7 @@
+6 3329
+Feltia.jacul.150 ATTTTATT------------------TAT--AAGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCCGGAATAGTAGGAACTTCACTAAGATTACTAATTCGAGCTGAATTAGGAAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTACCTTTAATATTAGGAGCCCCAGATATAGCATTCCCTCGAATAAATAATATAAGTTTTTGACTTCTTCCCCCATCTTTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGAACAGGTTGAACAGTGTACCCCCCACTTTCTTCTAATATTGCCCATGGAGGTAGATCTGTAGATCTTACTATTTTTTCCC [...]
+Lambdina.fisc.9 ATTTTATTTATTATTAAATCAATACAATATCAAGCGAAAATGACTTTATTCAACAAATCATAAAGATATTGGGACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTTGGAACTTCTTTAAGACTTTTAATTCGGGCAGAATTAGGTAACCCTGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTAACCGCTCATGCTTTTATTATAATTTTCTTTATAGTTATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTTCCTTTAATATTAGGGGCTCCTGACATAGCTTTTCCTCGTATAAATAATATAAGATTTTGATTATTACCTCCCTCTCTTACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGGGCTGGGACTGGATGAACTGTTTACCCTCCTTTATCTTCTAATATCGCTCACGGAGGAAGCTCTGTAGATTTAGCAATTTTCTCCT [...]
+Ostrinia.nub.5 ATTTTATT------------------TTAATTAGCGAAAATGACTATATTCAACAAATCATAAAGATATTGGAACTTTATATTTTATTTTTGGAATTTGAAGAGGAATAGTAGGAACTTCTCTAAGTTTATTAATTCGAGCTGAATTAGGTAATCCTGGATCATTAATTGGAGATGATCAAATTTATAATACAATTGTAACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTACCTCTAATATTAGGAGCTCCTGATATAGCATTCCCACGAATAAATAATATAAGATTTTGATTATTACCCCCATCATTAACCCTTTTAATTTCAAGAAGAATCGTTGAAAATGGAGCAGGAACTGGTTGAACTGTTTACCCCCCACTTTCATCTAATATTGCTCATGGAGGTAGATCTGTAGACCTAGCTATTTTTTCAT [...]
+Proserp.clark.988 ATTTTATT------------------------AGCGAAAATGACTTTATTCTACAAATCATAAAGATATTGGAACATTATATTTTAATTTTGGAATTTGAGCTGGAATAGTAGGAACTTCATTAAGTTTATTAATTCGAGCAGAATTAGGAAATCCTGGATCTTTAATTGGAGATGACCAAATTTATAATACAATTGTTACAGCTCATGCATTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGTGGATTTGGAAATTGATTAGTTCCTTTAATATTAGGAGCTCCTGATATAGCATTCCCCCGAATAAATAATATAAGATTTTGATTATTACCCCCATCTTTAACTCTACTTATTTCTAGAAGTATTGTAGAAAATGGAGCTGGAACTGGATGAACAGTATACCCCCCTCTATCCTCTAATATTGCTCATAGAGGAAGATCTGTTGATCTAGCAATTTTCTCCC [...]
+Macrosoma.983 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATATTTTATTTTTGGAATTTGAGCAGGAATAGTAGGAACCTCATTAAGTTTACTTATTCGAACTGAATTAGGTAATCCAGGATCATTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCATGCTTTTATTATAATTTTTTTTATAGTAATACCTATTATAATTGGAGGATTTGGTAATTGATTAGTCCCTTTAATATTAGGAGCTCCTGATATAGCTTTTCCCCGAATAAATAATATAAGATTTTGACTTCTACCCCCATCATTAACTTTATTAATTTCAAGAAGAATTGTAGAAAATGGAGCAGGTACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCATAGAGGAGCATCTGTTGATTTAGCTATTTTTTCAC [...]
+Euphil.bern.969 ATTTTATT------------------------AGCGAAAATGACTTTTTTCTACAAATCATAAAGATATTGGAACATTATACTTTATTTTTGGTATTTGAGCAGGAATAGTAGGAACATCCCTAAGAATTTTAATTCGTATAGAATTAGGAAATCCCGGATCTTTAATTGGAGATGATCAAATTTATAATACTATTGTTACAGCTCACGCATTTATTATAATTTTTTTTATAGTTATACCTATTATAATTGGTGGATTTGGTAATTGATTAGTGCCTTTAATATTAGGGGCACCTGATATAGCTTTCCCCCGAATAAATAATATAAGATTTTGATTATTACCACCATCATTAATATTATTAATTTCTAGAAGAATTGTAGAAAATGGAGCAGGAACAGGATGAACAGTTTACCCCCCACTTTCATCTAATATTGCCCACAGAGGATCATCTGTAGACTTAGCAATTTTTTCTC [...]
diff --git a/tests/misc/interleave.phy b/tests/misc/interleave.phy
new file mode 100644
index 0000000..b0e0642
--- /dev/null
+++ b/tests/misc/interleave.phy
@@ -0,0 +1,133 @@
+10 705
+Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA
+Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT
+Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC
+Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT
+Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT
+Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA
+Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT
+Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA
+Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC
+Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA
+
+CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC
+CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT
+GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC
+ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT
+CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT
+ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT
+ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT
+CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC
+CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC
+CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC
+
+ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA
+ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA
+CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA
+GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA
+GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA
+ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA
+ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA
+ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA
+ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA
+ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG
+
+GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT
+ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC
+GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC
+ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC
+ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA
+GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT
+GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC
+GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA
+GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA
+ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC
+
+TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA
+CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA
+CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC
+CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT
+CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG
+CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA
+CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA
+TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA
+TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA
+CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC
+
+GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC
+GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC
+GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC
+GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC
+GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC
+GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA
+GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC
+GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA
+GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC
+GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT
+
+TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT
+TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC
+TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT
+TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT
+TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC
+TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC
+TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT
+TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT
+TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC
+TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT
+
+CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA
+CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA
+CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC
+CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG
+CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA
+CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC
+CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG
+CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC
+CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC
+CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC
+
+CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC
+CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT
+CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT
+CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC
+CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC
+CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT
+CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC
+CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC
+CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC
+CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT
+
+CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC
+CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT
+CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC
+CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT
+CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT
+CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT
+CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC
+CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT
+CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC
+CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC
+
+GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA
+GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA
+GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA
+GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA
+GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA
+GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA
+GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA
+GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG
+GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA
+GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA
+
+AAATGATCTGCGTCAATATTA---------------------TAA
+AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA
+GCCTGATCCTCACTA------------------CTGTCATCTTAA
+ATA---------------------GGGCCCGTATTTACCCTATAG
+AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA
+AACTGATCTGCTTCAATAATT---------------------TAA
+AACTGATCAGCTTCTATAATT---------------------TAA
+AAATGATCTACCTCAATGCTT---------------------TAA
+AAATGATCTGTATCAATACTA---------------------TAA
+AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA
+
diff --git a/tests/misc/raxml_aminoacid.output b/tests/misc/raxml_aminoacid.output
new file mode 100644
index 0000000..7cfee2d
--- /dev/null
+++ b/tests/misc/raxml_aminoacid.output
@@ -0,0 +1,301 @@
+IMPORTANT WARNING: Alignment column 316 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 317 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 318 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 319 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 320 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 321 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 322 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 323 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 324 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 325 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 326 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 327 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 328 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 329 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 330 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 331 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 332 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 333 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 334 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 335 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 336 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 472 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 473 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 474 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 475 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 476 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 477 contains only undetermined values which will be treated as missing data
+
+IMPORTANT WARNING
+Found 27 columns that contain only undetermined values which will be treated as missing data.
+Normally these columns should be excluded from the analysis.
+
+An alignment file with undetermined columns removed has already
+been printed to file ./analysis/phyml/37ef7d6aa18a90886723b5bb7366b4c1.phy.reduced
+
+
+This is RAxML version 7.3.9 released by Alexandros Stamatakis on November 8 2012.
+
+With greatly appreciated code contributions by:
+Andre Aberer (HITS)
+Simon Berger (HITS)
+Nick Pattengale (Sandia)
+Wayne Pfeiffer (SDSC)
+Akifumi S. Tanabe (Univ. Tsukuba)
+
+
+Alignment has 71 distinct alignment patterns
+
+Proportion of gaps and completely undetermined characters in this alignment: 8.21%
+
+RAxML Branch length scaler and other model parameter optimization up to an accuracy of 1.000000 log likelihood units
+
+Using 1 distinct models/data partitions with individual per partition branch length optimization
+
+
+All free model parameters will be estimated by RAxML
+GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter
+
+GAMMA Model parameters will be estimated up to an accuracy of 1.0000000000 Log Likelihood units
+
+Partition: 0
+Alignment Patterns: 71
+Name: No Name Provided
+DataType: AA
+Substitution Matrix: BLOSUM62
+Using empirical base frequencies
+
+
+
+
+RAxML was called as follows:
+
+/Users/Brett/Code/partitionfinder/programs/raxml -f B -s ./analysis/phyml/37ef7d6aa18a90886723b5bb7366b4c1.phy -t ./analysis/start_tree/RAxML_result.BLTREE -m PROTGAMMABLOSUM62F -n 37ef7d6aa18a90886723b5bb7366b4c1_BLOSUM62+G+F.txt -w /Users/Brett/Code/partitionfinder/examples/aminoacid/analysis/phyml -e 1.0 -T 2 -O
+
+
+Likelihood: -1751.003114
+
+
+Overall Time for Tree Evaluation with branch length scalers: 0.019206
+Final GAMMA likelihood: -1751.003114
+
+Number of free parameters for AIC-TEST(BR-LEN): 21
+Number of free parameters for AIC-TEST(NO-BR-LEN): 20
+
+
+Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
+alpha: 2.387812
+Branch length scaler: 1.431846
+Tree-Length: 0.025301
+rate A <-> R: 0.885232
+rate A <-> N : 0.583975
+rate A <-> D: 0.653480
+rate A <-> C: 1.756525
+rate A <-> Q: 1.443370
+rate A <-> E: 1.408772
+rate A <-> G: 2.353130
+rate A <-> H: 0.861712
+rate A <-> I: 0.728959
+rate A <-> L: 0.962502
+rate A <-> K: 1.558261
+rate A <-> M: 1.508400
+rate A <-> F: 0.593087
+rate A <-> P: 1.411572
+rate A <-> S: 5.203533
+rate A <-> T: 2.080379
+rate A <-> W: 0.560453
+rate A <-> Y: 0.864077
+rate A <-> V: 2.632118
+rate R <-> N : 1.560962
+rate R <-> D: 0.602712
+rate R <-> C: 0.274099
+rate R <-> Q: 3.634374
+rate R <-> E: 1.636911
+rate R <-> G: 0.503815
+rate R <-> H: 1.751888
+rate R <-> I: 0.279164
+rate R <-> L: 0.749186
+rate R <-> K: 6.510130
+rate R <-> M: 1.183484
+rate R <-> F: 0.447127
+rate R <-> P: 0.539151
+rate R <-> S: 1.350824
+rate R <-> T: 1.100437
+rate R <-> W: 0.512982
+rate R <-> Y: 0.866857
+rate R <-> V: 0.527426
+rate N <-> D: 3.825988
+rate N <-> C: 0.478064
+rate N <-> Q: 2.212767
+rate N <-> E: 1.492436
+rate N <-> G: 1.631254
+rate N <-> H: 2.904894
+rate N <-> I: 0.340499
+rate N <-> L: 0.254923
+rate N <-> K: 1.916708
+rate N <-> M: 0.780142
+rate N <-> F: 0.426935
+rate N <-> P: 0.595400
+rate N <-> S: 3.493934
+rate N <-> T: 2.283699
+rate N <-> W: 0.230373
+rate N <-> Y: 0.647537
+rate N <-> V: 0.376401
+rate D <-> C: 0.289751
+rate D <-> Q: 1.432831
+rate D <-> E: 4.525623
+rate D <-> G: 0.960646
+rate D <-> H: 0.936186
+rate D <-> I: 0.503566
+rate D <-> L: 0.262435
+rate D <-> K: 1.242141
+rate D <-> M: 0.267837
+rate D <-> F: 0.338951
+rate D <-> P: 0.879021
+rate D <-> S: 1.904216
+rate D <-> T: 1.123924
+rate D <-> W: 0.174865
+rate D <-> Y: 0.314518
+rate D <-> V: 0.310556
+rate C <-> Q: 0.396785
+rate C <-> E: 0.169335
+rate C <-> G: 0.503142
+rate C <-> H: 0.425968
+rate C <-> I: 0.932277
+rate C <-> L: 1.000792
+rate C <-> K: 0.342979
+rate C <-> M: 0.923609
+rate C <-> F: 0.530974
+rate C <-> P: 0.428315
+rate C <-> S: 1.440341
+rate C <-> T: 1.347273
+rate C <-> W: 0.634835
+rate C <-> Y: 0.565744
+rate C <-> V: 1.343087
+rate Q <-> E: 6.651860
+rate Q <-> G: 0.733708
+rate Q <-> H: 2.929967
+rate Q <-> I: 0.284176
+rate Q <-> L: 0.698687
+rate Q <-> K: 4.746576
+rate Q <-> M: 3.001617
+rate Q <-> F: 0.173676
+rate Q <-> P: 1.032949
+rate Q <-> S: 2.327849
+rate Q <-> T: 1.536941
+rate Q <-> W: 0.912739
+rate Q <-> Y: 1.153764
+rate Q <-> V: 0.638590
+rate E <-> G: 0.509610
+rate E <-> H: 1.957318
+rate E <-> I: 0.224797
+rate E <-> L: 0.448307
+rate E <-> K: 3.371609
+rate E <-> M: 0.668222
+rate E <-> F: 0.350595
+rate E <-> P: 1.114752
+rate E <-> S: 2.129364
+rate E <-> T: 1.288640
+rate E <-> W: 0.490428
+rate E <-> Y: 0.717915
+rate E <-> V: 0.630731
+rate G <-> H: 0.649506
+rate G <-> I: 0.227743
+rate G <-> L: 0.261941
+rate G <-> K: 0.904785
+rate G <-> M: 0.552749
+rate G <-> F: 0.442942
+rate G <-> P: 0.606468
+rate G <-> S: 1.815875
+rate G <-> T: 0.771714
+rate G <-> W: 0.611608
+rate G <-> Y: 0.370623
+rate G <-> V: 0.304795
+rate H <-> I: 0.304046
+rate H <-> L: 0.418767
+rate H <-> K: 1.230181
+rate H <-> M: 1.184228
+rate H <-> F: 0.859658
+rate H <-> P: 0.634044
+rate H <-> S: 1.343902
+rate H <-> T: 0.704305
+rate H <-> W: 0.362433
+rate H <-> Y: 5.075837
+rate H <-> V: 0.242493
+rate I <-> L: 4.681231
+rate I <-> K: 0.488693
+rate I <-> M: 4.048199
+rate I <-> F: 1.825540
+rate I <-> P: 0.467232
+rate I <-> S: 0.430163
+rate I <-> T: 1.418568
+rate I <-> W: 0.411444
+rate I <-> Y: 0.811634
+rate I <-> V: 10.000000
+rate L <-> K: 0.536067
+rate L <-> M: 7.255385
+rate L <-> F: 2.484215
+rate L <-> P: 0.450629
+rate L <-> S: 0.424658
+rate L <-> T: 1.101152
+rate L <-> W: 0.831915
+rate L <-> Y: 0.976012
+rate L <-> V: 2.684611
+rate K <-> M: 1.291003
+rate K <-> F: 0.321138
+rate K <-> P: 1.260110
+rate K <-> S: 2.108036
+rate K <-> T: 1.568696
+rate K <-> W: 0.399723
+rate K <-> Y: 0.863820
+rate K <-> V: 0.599312
+rate M <-> F: 2.134131
+rate M <-> P: 0.546358
+rate M <-> S: 1.105319
+rate M <-> T: 1.790877
+rate M <-> W: 1.068477
+rate M <-> Y: 1.144972
+rate M <-> V: 3.099014
+rate F <-> P: 0.281042
+rate F <-> S: 0.649709
+rate F <-> T: 0.587362
+rate F <-> W: 2.495627
+rate F <-> Y: 8.117650
+rate F <-> V: 1.008344
+rate P <-> S: 1.406583
+rate P <-> T: 1.209662
+rate P <-> W: 0.303440
+rate P <-> Y: 0.444433
+rate P <-> V: 0.597832
+rate S <-> T: 6.197853
+rate S <-> W: 0.466715
+rate S <-> Y: 0.958574
+rate S <-> V: 0.676054
+rate T <-> W: 0.617346
+rate T <-> Y: 0.963698
+rate T <-> V: 2.710680
+rate W <-> Y: 4.877884
+rate W <-> V: 0.320637
+rate Y <-> V: 1.203103
+
+freq pi(A): 0.046704
+freq pi(R): 0.017460
+freq pi(N ): 0.068093
+freq pi(D): 0.030991
+freq pi(C): 0.003492
+freq pi(Q): 0.021388
+freq pi(E): 0.027499
+freq pi(G): 0.064164
+freq pi(H): 0.027499
+freq pi(I): 0.131820
+freq pi(L): 0.121781
+freq pi(K): 0.019642
+freq pi(M): 0.061545
+freq pi(F): 0.073330
+freq pi(P): 0.035356
+freq pi(S): 0.102139
+freq pi(T): 0.048014
+freq pi(W): 0.025753
+freq pi(Y): 0.035356
+freq pi(V): 0.037975
+
diff --git a/tests/misc/raxml_aminoacid_LG4M+G.output b/tests/misc/raxml_aminoacid_LG4M+G.output
new file mode 100644
index 0000000..762966f
--- /dev/null
+++ b/tests/misc/raxml_aminoacid_LG4M+G.output
@@ -0,0 +1,942 @@
+IMPORTANT WARNING: Alignment column 16 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 17 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 18 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 19 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 20 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 21 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 22 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 23 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 24 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 25 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 26 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 27 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 28 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 29 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 30 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 31 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 32 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 33 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 34 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 35 contains only undetermined values which will be treated as missing data
+IMPORTANT WARNING: Alignment column 36 contains only undetermined values which will be treated as missing data
+
+IMPORTANT WARNING
+Found 21 columns that contain only undetermined values which will be treated as missing data.
+Normally these columns should be excluded from the analysis.
+
+An alignment file with undetermined columns removed has already
+been printed to file ./analysis/phylofiles/a8d53b0f5f557a9337ac4c910c33bb54.phy.reduced
+
+Alignment has 21 completely undetermined sites that will be automatically removed from the input data
+
+
+
+This is RAxML version 8.2.2 released by Alexandros Stamatakis on August 6 2015.
+
+With greatly appreciated code contributions by:
+Andre Aberer (HITS)
+Simon Berger (HITS)
+Alexey Kozlov (HITS)
+Kassian Kobert (HITS)
+David Dao (KIT and HITS)
+Nick Pattengale (Sandia)
+Wayne Pfeiffer (SDSC)
+Akifumi S. Tanabe (NRIFS)
+
+Alignment has 40 distinct alignment patterns
+
+Proportion of gaps and completely undetermined characters in this alignment: 26.90%
+
+RAxML Branch length scaler and other model parameter optimization up to an accuracy of 1.000000 log likelihood units
+
+Using 1 distinct models/data partitions with individual per partition branch length optimization
+
+
+All free model parameters will be estimated by RAxML
+GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter
+
+GAMMA Model parameters will be estimated up to an accuracy of 1.0000000000 Log Likelihood units
+
+Partition: 0
+Alignment Patterns: 40
+Name: No Name Provided
+DataType: AA
+Substitution Matrix: LG4M
+Using fixed base frequencies
+
+
+
+
+RAxML was called as follows:
+
+/Users/brett/Dropbox/Code/partitionfinder/programs/raxml -f B -s ./analysis/phylofiles/a8d53b0f5f557a9337ac4c910c33bb54.phy -t ./analysis/start_tree/RAxML_result.BLTREE -m PROTGAMMALG4M -n a8d53b0f5f557a9337ac4c910c33bb54_LG4M+G.txt -w /Users/brett/Dropbox/Code/partitionfinder/tests/clustering/prot_hcluster2/analysis/phylofiles -e 1.0 -O
+
+
+Likelihood: -318.641970
+
+
+Overall Time for Tree Evaluation with branch length scalers: 0.121495
+Final GAMMA likelihood: -318.641970
+
+Number of free parameters for AIC-TEST(BR-LEN): 2
+Number of free parameters for AIC-TEST(NO-BR-LEN): 1
+
+
+Model Parameters of Partition 0, Name: No Name Provided, Type of Data: AA
+alpha: 4.988615
+Branch length scaler: 1.702259
+Tree-Length: 0.128950
+
+LG4X rates: 0.501604 0.803687 1.083322 1.611387
+
+LG4X weights: 0.250000 0.250000 0.250000 0.250000
+
+LGM 0
+rate A <-> R: 0.104937
+rate A <-> N: 0.099198
+rate A <-> D: 0.092266
+rate A <-> C: 0.976558
+rate A <-> Q: 0.139899
+rate A <-> E: 0.118702
+rate A <-> G: 0.659214
+rate A <-> H: 0.098170
+rate A <-> I: 0.422805
+rate A <-> L: 0.263509
+rate A <-> K: 0.069799
+rate A <-> M: 0.637709
+rate A <-> F: 0.091751
+rate A <-> P: 0.493083
+rate A <-> S: 2.091546
+rate A <-> T: 0.599752
+rate A <-> W: 0.054912
+rate A <-> Y: 0.077857
+rate A <-> V: 3.676110
+rate R <-> N: 0.058825
+rate R <-> D: 0.012414
+rate R <-> C: 0.365679
+rate R <-> Q: 0.135694
+rate R <-> E: 0.060778
+rate R <-> G: 0.111675
+rate R <-> H: 0.359071
+rate R <-> I: 0.126864
+rate R <-> L: 0.234684
+rate R <-> K: 0.378436
+rate R <-> M: 0.200730
+rate R <-> F: 0.048284
+rate R <-> P: 0.015648
+rate R <-> S: 0.183484
+rate R <-> T: 0.127318
+rate R <-> W: 0.146339
+rate R <-> Y: 0.057216
+rate R <-> V: 0.111401
+rate N <-> D: 0.257001
+rate N <-> C: 0.380150
+rate N <-> Q: 0.271829
+rate N <-> E: 0.147155
+rate N <-> G: 0.220163
+rate N <-> H: 0.493864
+rate N <-> I: 0.318952
+rate N <-> L: 0.084554
+rate N <-> K: 0.523516
+rate N <-> M: 0.261214
+rate N <-> F: 0.038880
+rate N <-> P: 0.067539
+rate N <-> S: 2.052093
+rate N <-> T: 0.657716
+rate N <-> W: 0.009804
+rate N <-> Y: 0.314127
+rate N <-> V: 0.154154
+rate D <-> C: 0.068388
+rate D <-> Q: 0.033729
+rate D <-> E: 0.174986
+rate D <-> G: 0.148189
+rate D <-> H: 0.120657
+rate D <-> I: 0.014732
+rate D <-> L: 0.002935
+rate D <-> K: 0.052107
+rate D <-> M: 0.027760
+rate D <-> F: 0.011854
+rate D <-> P: 0.010745
+rate D <-> S: 0.304087
+rate D <-> T: 0.110545
+rate D <-> W: 0.001074
+rate D <-> Y: 0.091263
+rate D <-> V: 0.050995
+rate C <-> Q: 0.037389
+rate C <-> E: 0.025210
+rate C <-> G: 0.240753
+rate C <-> H: 0.152112
+rate C <-> I: 0.445764
+rate C <-> L: 0.621719
+rate C <-> K: 0.047714
+rate C <-> M: 0.597981
+rate C <-> F: 0.349583
+rate C <-> P: 0.101282
+rate C <-> S: 1.942588
+rate C <-> T: 0.541268
+rate C <-> W: 0.312250
+rate C <-> Y: 0.559848
+rate C <-> V: 2.375512
+rate Q <-> E: 1.691888
+rate Q <-> G: 0.078722
+rate Q <-> H: 0.913252
+rate Q <-> I: 0.208269
+rate Q <-> L: 0.261479
+rate Q <-> K: 0.383314
+rate Q <-> M: 2.060470
+rate Q <-> F: 0.043725
+rate Q <-> P: 0.226115
+rate Q <-> S: 0.346962
+rate Q <-> T: 0.128499
+rate Q <-> W: 0.100227
+rate Q <-> Y: 0.124544
+rate Q <-> V: 0.201136
+rate E <-> G: 0.102988
+rate E <-> H: 0.084836
+rate E <-> I: 0.086801
+rate E <-> L: 0.061722
+rate E <-> K: 0.387315
+rate E <-> M: 0.099593
+rate E <-> F: 0.008777
+rate E <-> P: 0.034301
+rate E <-> S: 0.147250
+rate E <-> T: 0.090298
+rate E <-> W: 0.040393
+rate E <-> Y: 0.003926
+rate E <-> V: 0.196229
+rate G <-> H: 0.040847
+rate G <-> I: 0.024421
+rate G <-> L: 0.027453
+rate G <-> K: 0.086070
+rate G <-> M: 0.036700
+rate G <-> F: 0.018501
+rate G <-> P: 0.056724
+rate G <-> S: 0.683954
+rate G <-> T: 0.045590
+rate G <-> W: 0.051815
+rate G <-> Y: 0.014360
+rate G <-> V: 0.086866
+rate H <-> I: 0.221073
+rate H <-> L: 0.297756
+rate H <-> K: 0.159964
+rate H <-> M: 0.100217
+rate H <-> F: 0.297234
+rate H <-> P: 0.055977
+rate H <-> S: 0.306365
+rate H <-> T: 0.175312
+rate H <-> W: 0.134738
+rate H <-> Y: 1.364903
+rate H <-> V: 0.058107
+rate I <-> L: 3.205079
+rate I <-> K: 0.150966
+rate I <-> M: 10.000000
+rate I <-> F: 0.523727
+rate I <-> P: 0.116436
+rate I <-> S: 0.205417
+rate I <-> T: 1.375922
+rate I <-> W: 0.146941
+rate I <-> Y: 0.233229
+rate I <-> V: 5.324382
+rate L <-> K: 0.070561
+rate L <-> M: 2.656971
+rate L <-> F: 0.337276
+rate L <-> P: 0.397441
+rate L <-> S: 0.260170
+rate L <-> T: 0.281132
+rate L <-> W: 0.327129
+rate L <-> Y: 0.287904
+rate L <-> V: 1.164201
+rate K <-> M: 0.619941
+rate K <-> F: 0.015164
+rate K <-> P: 0.000278
+rate K <-> S: 0.257118
+rate K <-> T: 0.193862
+rate K <-> W: 0.068948
+rate K <-> Y: 0.060169
+rate K <-> V: 0.063398
+rate M <-> F: 0.791218
+rate M <-> P: 0.074032
+rate M <-> S: 0.285159
+rate M <-> T: 1.048693
+rate M <-> W: 0.197015
+rate M <-> Y: 0.225580
+rate M <-> V: 2.327420
+rate F <-> P: 0.036609
+rate F <-> S: 0.326358
+rate F <-> T: 0.059254
+rate F <-> W: 0.650703
+rate F <-> Y: 1.654069
+rate F <-> V: 0.328597
+rate P <-> S: 0.528157
+rate P <-> T: 0.271958
+rate P <-> W: 0.035570
+rate P <-> Y: 0.029035
+rate P <-> V: 0.232746
+rate S <-> T: 6.358826
+rate S <-> W: 0.081854
+rate S <-> Y: 0.176956
+rate S <-> V: 0.273170
+rate T <-> W: 0.005129
+rate T <-> Y: 0.090744
+rate T <-> V: 1.823342
+rate W <-> Y: 0.459143
+rate W <-> V: 0.116914
+rate Y <-> V: 0.162177
+
+freq pi(A): 0.082276
+freq pi(R): 0.055172
+freq pi(N): 0.043853
+freq pi(D): 0.053484
+freq pi(C): 0.018957
+freq pi(Q): 0.028152
+freq pi(E): 0.046679
+freq pi(G): 0.157817
+freq pi(H): 0.033297
+freq pi(I): 0.028284
+freq pi(L): 0.054284
+freq pi(K): 0.025275
+freq pi(M): 0.023665
+freq pi(F): 0.041874
+freq pi(P): 0.063071
+freq pi(S): 0.066501
+freq pi(T): 0.065424
+freq pi(W): 0.023837
+freq pi(Y): 0.038633
+freq pi(V): 0.049465
+LGM 1
+rate A <-> R: 0.108723
+rate A <-> N: 0.274175
+rate A <-> D: 0.090184
+rate A <-> C: 3.246944
+rate A <-> Q: 0.335044
+rate A <-> E: 0.353923
+rate A <-> G: 6.372433
+rate A <-> H: 0.165761
+rate A <-> I: 0.032293
+rate A <-> L: 0.061617
+rate A <-> K: 0.144451
+rate A <-> M: 0.342125
+rate A <-> F: 0.057946
+rate A <-> P: 0.779833
+rate A <-> S: 9.530356
+rate A <-> T: 2.314853
+rate A <-> W: 0.024557
+rate A <-> Y: 0.054624
+rate A <-> V: 0.552395
+rate R <-> N: 0.609028
+rate R <-> D: 0.085443
+rate R <-> C: 0.153104
+rate R <-> Q: 2.102403
+rate R <-> E: 0.161213
+rate R <-> G: 0.133836
+rate R <-> H: 1.732101
+rate R <-> I: 0.019963
+rate R <-> L: 0.065119
+rate R <-> K: 8.434503
+rate R <-> M: 0.156731
+rate R <-> F: 0.015978
+rate R <-> P: 1.216822
+rate R <-> S: 0.292222
+rate R <-> T: 0.177625
+rate R <-> W: 0.314894
+rate R <-> Y: 0.105781
+rate R <-> V: 0.033797
+rate N <-> D: 3.881157
+rate N <-> C: 1.293044
+rate N <-> Q: 1.550421
+rate N <-> E: 0.240965
+rate N <-> G: 0.351020
+rate N <-> H: 7.622065
+rate N <-> I: 0.109970
+rate N <-> L: 0.069087
+rate N <-> K: 0.842922
+rate N <-> M: 0.267942
+rate N <-> F: 0.072162
+rate N <-> P: 0.307171
+rate N <-> S: 1.950672
+rate N <-> T: 1.508550
+rate N <-> W: 0.096656
+rate N <-> Y: 0.283540
+rate N <-> V: 0.075134
+rate D <-> C: 0.247938
+rate D <-> Q: 0.356421
+rate D <-> E: 6.073870
+rate D <-> G: 0.125090
+rate D <-> H: 0.878825
+rate D <-> I: 0.012179
+rate D <-> L: 0.011487
+rate D <-> K: 0.031143
+rate D <-> M: 0.006774
+rate D <-> F: 0.011015
+rate D <-> P: 0.269946
+rate D <-> S: 0.178439
+rate D <-> T: 0.089281
+rate D <-> W: 0.054709
+rate D <-> Y: 0.050246
+rate D <-> V: 0.019270
+rate C <-> Q: 0.196824
+rate C <-> E: 0.006865
+rate C <-> G: 1.463287
+rate C <-> H: 0.123958
+rate C <-> I: 0.119926
+rate C <-> L: 0.250706
+rate C <-> K: 0.034986
+rate C <-> M: 0.718052
+rate C <-> F: 0.460690
+rate C <-> P: 0.258711
+rate C <-> S: 7.402304
+rate C <-> T: 3.534435
+rate C <-> W: 0.154678
+rate C <-> Y: 0.244894
+rate C <-> V: 1.033558
+rate Q <-> E: 2.679469
+rate Q <-> G: 0.219320
+rate Q <-> H: 10.000000
+rate Q <-> I: 0.027615
+rate Q <-> L: 0.407212
+rate Q <-> K: 1.773323
+rate Q <-> M: 1.140994
+rate Q <-> F: 0.058442
+rate Q <-> P: 1.127697
+rate Q <-> S: 0.624079
+rate Q <-> T: 0.622685
+rate Q <-> W: 0.099286
+rate Q <-> Y: 0.077552
+rate Q <-> V: 0.093963
+rate E <-> G: 0.197466
+rate E <-> H: 0.227324
+rate E <-> I: 0.004541
+rate E <-> L: 0.018565
+rate E <-> K: 0.261128
+rate E <-> M: 0.137142
+rate E <-> F: 0.016302
+rate E <-> P: 0.744690
+rate E <-> S: 0.191257
+rate E <-> T: 0.133805
+rate E <-> W: 0.005710
+rate E <-> Y: 0.077862
+rate E <-> V: 0.044944
+rate G <-> H: 0.072943
+rate G <-> I: 0.005893
+rate G <-> L: 0.018700
+rate G <-> K: 0.083786
+rate G <-> M: 0.130682
+rate G <-> F: 0.033354
+rate G <-> P: 0.182334
+rate G <-> S: 2.944288
+rate G <-> T: 0.253696
+rate G <-> W: 0.111724
+rate G <-> Y: 0.036285
+rate G <-> V: 0.070727
+rate H <-> I: 0.018494
+rate H <-> L: 0.131123
+rate H <-> K: 0.373605
+rate H <-> M: 0.498062
+rate H <-> F: 0.508459
+rate H <-> P: 2.123303
+rate H <-> S: 0.790263
+rate H <-> T: 0.188281
+rate H <-> W: 0.475758
+rate H <-> Y: 1.713441
+rate H <-> V: 0.049417
+rate I <-> L: 1.229096
+rate I <-> K: 0.017249
+rate I <-> M: 1.236582
+rate I <-> F: 0.311246
+rate I <-> P: 0.023864
+rate I <-> S: 0.027465
+rate I <-> T: 0.289717
+rate I <-> W: 0.016777
+rate I <-> Y: 0.037486
+rate I <-> V: 6.695730
+rate L <-> K: 0.063740
+rate L <-> M: 6.312043
+rate L <-> F: 1.433482
+rate L <-> P: 0.055492
+rate L <-> S: 0.034990
+rate L <-> T: 0.129763
+rate L <-> W: 0.186049
+rate L <-> Y: 0.081402
+rate L <-> V: 0.495498
+rate K <-> M: 0.250345
+rate K <-> F: 0.036298
+rate K <-> P: 1.254036
+rate K <-> S: 0.192639
+rate K <-> T: 0.327836
+rate K <-> W: 0.000099
+rate K <-> Y: 0.013881
+rate K <-> V: 0.050218
+rate M <-> F: 1.261805
+rate M <-> P: 0.038641
+rate M <-> S: 0.260152
+rate M <-> T: 0.922961
+rate M <-> W: 0.386094
+rate M <-> Y: 0.156420
+rate M <-> V: 0.473173
+rate F <-> P: 0.148559
+rate F <-> S: 0.101614
+rate F <-> T: 0.086919
+rate F <-> W: 2.549064
+rate F <-> Y: 6.803440
+rate F <-> V: 0.149756
+rate P <-> S: 0.683504
+rate P <-> T: 0.218869
+rate P <-> W: 0.024646
+rate P <-> Y: 0.000762
+rate P <-> V: 0.065245
+rate S <-> T: 7.981441
+rate S <-> W: 0.076290
+rate S <-> Y: 0.111728
+rate S <-> V: 0.079707
+rate T <-> W: 0.096878
+rate T <-> Y: 0.036362
+rate T <-> V: 1.169473
+rate W <-> Y: 3.398436
+rate W <-> V: 0.019057
+rate Y <-> V: 0.031810
+
+freq pi(A): 0.120900
+freq pi(R): 0.036460
+freq pi(N): 0.026510
+freq pi(D): 0.040410
+freq pi(C): 0.015980
+freq pi(Q): 0.021132
+freq pi(E): 0.025191
+freq pi(G): 0.036369
+freq pi(H): 0.015884
+freq pi(I): 0.111029
+freq pi(L): 0.162852
+freq pi(K): 0.024820
+freq pi(M): 0.028023
+freq pi(F): 0.074058
+freq pi(P): 0.012065
+freq pi(S): 0.041963
+freq pi(T): 0.039072
+freq pi(W): 0.012666
+freq pi(Y): 0.040478
+freq pi(V): 0.114137
+LGM 2
+rate A <-> R: 0.290232
+rate A <-> N: 0.218000
+rate A <-> D: 0.197146
+rate A <-> C: 2.780895
+rate A <-> Q: 0.611442
+rate A <-> E: 0.524275
+rate A <-> G: 0.519848
+rate A <-> H: 0.393915
+rate A <-> I: 0.111781
+rate A <-> L: 0.212327
+rate A <-> K: 0.268961
+rate A <-> M: 0.718517
+rate A <-> F: 0.249876
+rate A <-> P: 1.210163
+rate A <-> S: 2.740242
+rate A <-> T: 1.768260
+rate A <-> W: 0.195524
+rate A <-> Y: 0.167178
+rate A <-> V: 1.927322
+rate R <-> N: 0.477960
+rate R <-> D: 0.041311
+rate R <-> C: 0.935947
+rate R <-> Q: 1.924429
+rate R <-> E: 0.160656
+rate R <-> G: 0.277739
+rate R <-> H: 1.598935
+rate R <-> I: 0.058753
+rate R <-> L: 0.197881
+rate R <-> K: 5.282700
+rate R <-> M: 0.251306
+rate R <-> F: 0.050626
+rate R <-> P: 0.060009
+rate R <-> S: 0.615872
+rate R <-> T: 0.368156
+rate R <-> W: 0.343250
+rate R <-> Y: 0.137291
+rate R <-> V: 0.073851
+rate N <-> D: 4.245222
+rate N <-> C: 0.488127
+rate N <-> Q: 1.173171
+rate N <-> E: 0.261076
+rate N <-> G: 1.535507
+rate N <-> H: 3.846603
+rate N <-> I: 0.065966
+rate N <-> L: 0.039289
+rate N <-> K: 1.146845
+rate N <-> M: 0.202135
+rate N <-> F: 0.089096
+rate N <-> P: 0.068471
+rate N <-> S: 3.788932
+rate N <-> T: 1.477980
+rate N <-> W: 0.052015
+rate N <-> Y: 0.325520
+rate N <-> V: 0.041988
+rate D <-> C: 0.043891
+rate D <-> Q: 0.333889
+rate D <-> E: 2.779954
+rate D <-> G: 0.760148
+rate D <-> H: 0.610342
+rate D <-> I: 0.004225
+rate D <-> L: 0.004896
+rate D <-> K: 0.072472
+rate D <-> M: 0.026184
+rate D <-> F: 0.013841
+rate D <-> P: 0.112929
+rate D <-> S: 0.963250
+rate D <-> T: 0.283594
+rate D <-> W: 0.030190
+rate D <-> Y: 0.059241
+rate D <-> V: 0.020490
+rate C <-> Q: 0.285592
+rate C <-> E: 0.056512
+rate C <-> G: 0.287170
+rate C <-> H: 0.992177
+rate C <-> I: 0.338432
+rate C <-> L: 0.661087
+rate C <-> K: 0.093083
+rate C <-> M: 1.024746
+rate C <-> F: 1.373536
+rate C <-> P: 0.167411
+rate C <-> S: 2.464540
+rate C <-> T: 1.571106
+rate C <-> W: 0.920516
+rate C <-> Y: 1.406145
+rate C <-> V: 2.058719
+rate Q <-> E: 3.405716
+rate Q <-> G: 0.316675
+rate Q <-> H: 2.827735
+rate Q <-> I: 0.072274
+rate Q <-> L: 0.399132
+rate Q <-> K: 2.319330
+rate Q <-> M: 1.159330
+rate Q <-> F: 0.078965
+rate Q <-> P: 0.222621
+rate Q <-> S: 0.954967
+rate Q <-> T: 0.615601
+rate Q <-> W: 0.212740
+rate Q <-> Y: 0.181130
+rate Q <-> V: 0.135988
+rate E <-> G: 0.350476
+rate E <-> H: 0.397584
+rate E <-> I: 0.031375
+rate E <-> L: 0.046269
+rate E <-> K: 0.449888
+rate E <-> M: 0.132642
+rate E <-> F: 0.016043
+rate E <-> P: 0.043390
+rate E <-> S: 0.397202
+rate E <-> T: 0.364125
+rate E <-> W: 0.096605
+rate E <-> Y: 0.058305
+rate E <-> V: 0.135788
+rate G <-> H: 0.295596
+rate G <-> I: 0.003243
+rate G <-> L: 0.016822
+rate G <-> K: 0.315521
+rate G <-> M: 0.048598
+rate G <-> F: 0.044457
+rate G <-> P: 0.136974
+rate G <-> S: 1.194857
+rate G <-> T: 0.093567
+rate G <-> W: 0.103953
+rate G <-> Y: 0.022230
+rate G <-> V: 0.030557
+rate H <-> I: 0.068201
+rate H <-> L: 0.236438
+rate H <-> K: 0.567807
+rate H <-> M: 0.153469
+rate H <-> F: 1.028381
+rate H <-> P: 0.132980
+rate H <-> S: 0.704011
+rate H <-> T: 0.357599
+rate H <-> W: 0.971807
+rate H <-> Y: 5.351027
+rate H <-> V: 0.080483
+rate I <-> L: 2.623374
+rate I <-> K: 0.089519
+rate I <-> M: 3.122535
+rate I <-> F: 0.767558
+rate I <-> P: 0.043394
+rate I <-> S: 0.044899
+rate I <-> T: 0.670513
+rate I <-> W: 0.082632
+rate I <-> Y: 0.106138
+rate I <-> V: 4.924993
+rate L <-> K: 0.100391
+rate L <-> M: 3.296327
+rate L <-> F: 1.469717
+rate L <-> P: 0.124280
+rate L <-> S: 0.089007
+rate L <-> T: 0.193503
+rate L <-> W: 0.564124
+rate L <-> Y: 0.206689
+rate L <-> V: 1.274364
+rate K <-> M: 0.458636
+rate K <-> F: 0.028730
+rate K <-> P: 0.041124
+rate K <-> S: 0.413828
+rate K <-> T: 0.613589
+rate K <-> W: 0.055556
+rate K <-> Y: 0.080831
+rate K <-> V: 0.081358
+rate M <-> F: 1.329535
+rate M <-> P: 0.089150
+rate M <-> S: 0.266972
+rate M <-> T: 1.260668
+rate M <-> W: 0.734868
+rate M <-> Y: 0.302087
+rate M <-> V: 1.378508
+rate F <-> P: 0.045345
+rate F <-> S: 0.307455
+rate F <-> T: 0.130308
+rate F <-> W: 2.588326
+rate F <-> Y: 10.000000
+rate F <-> V: 0.486513
+rate P <-> S: 0.895128
+rate P <-> T: 0.388645
+rate P <-> W: 0.050609
+rate P <-> Y: 0.061477
+rate P <-> V: 0.188032
+rate S <-> T: 5.368827
+rate S <-> W: 0.299903
+rate S <-> Y: 0.243182
+rate S <-> V: 0.066823
+rate T <-> W: 0.135991
+rate T <-> Y: 0.148500
+rate T <-> V: 1.255310
+rate W <-> Y: 3.484188
+rate W <-> V: 0.149596
+rate Y <-> V: 0.119242
+
+freq pi(A): 0.072639
+freq pi(R): 0.051691
+freq pi(N): 0.038642
+freq pi(D): 0.055580
+freq pi(C): 0.009829
+freq pi(Q): 0.031374
+freq pi(E): 0.048731
+freq pi(G): 0.065283
+freq pi(H): 0.023791
+freq pi(I): 0.086640
+freq pi(L): 0.120847
+freq pi(K): 0.052177
+freq pi(M): 0.026728
+freq pi(F): 0.032589
+freq pi(P): 0.039238
+freq pi(S): 0.046748
+freq pi(T): 0.053361
+freq pi(W): 0.008024
+freq pi(Y): 0.037426
+freq pi(V): 0.098662
+LGM 3
+rate A <-> R: 0.216909
+rate A <-> N: 0.213689
+rate A <-> D: 0.310350
+rate A <-> C: 0.309734
+rate A <-> Q: 0.472188
+rate A <-> E: 0.458777
+rate A <-> G: 0.678949
+rate A <-> H: 0.194585
+rate A <-> I: 0.068103
+rate A <-> L: 0.170203
+rate A <-> K: 0.250049
+rate A <-> M: 0.325430
+rate A <-> F: 0.122157
+rate A <-> P: 0.403973
+rate A <-> S: 1.444742
+rate A <-> T: 0.792864
+rate A <-> W: 0.061636
+rate A <-> Y: 0.090793
+rate A <-> V: 0.686909
+rate R <-> N: 0.187726
+rate R <-> D: 0.019086
+rate R <-> C: 1.705139
+rate R <-> Q: 0.816876
+rate R <-> E: 0.058166
+rate R <-> G: 0.227644
+rate R <-> H: 1.082086
+rate R <-> I: 0.167375
+rate R <-> L: 0.326148
+rate R <-> K: 1.092861
+rate R <-> M: 0.314374
+rate R <-> F: 0.078663
+rate R <-> P: 0.065441
+rate R <-> S: 0.332932
+rate R <-> T: 0.282361
+rate R <-> W: 0.307994
+rate R <-> Y: 0.113861
+rate R <-> V: 0.164065
+rate N <-> D: 1.242891
+rate N <-> C: 0.486332
+rate N <-> Q: 0.537597
+rate N <-> E: 0.154908
+rate N <-> G: 0.800194
+rate N <-> H: 1.824305
+rate N <-> I: 0.207425
+rate N <-> L: 0.075684
+rate N <-> K: 0.791337
+rate N <-> M: 0.238176
+rate N <-> F: 0.105540
+rate N <-> P: 0.015806
+rate N <-> S: 1.721205
+rate N <-> T: 0.874671
+rate N <-> W: 0.027227
+rate N <-> Y: 0.397216
+rate N <-> V: 0.067421
+rate D <-> C: 0.038374
+rate D <-> Q: 0.169215
+rate D <-> E: 1.194279
+rate D <-> G: 0.480525
+rate D <-> H: 0.270938
+rate D <-> I: 0.008863
+rate D <-> L: 0.010064
+rate D <-> K: 0.048184
+rate D <-> M: 0.029817
+rate D <-> F: 0.015693
+rate D <-> P: 0.101774
+rate D <-> S: 0.354921
+rate D <-> T: 0.126463
+rate D <-> W: 0.025704
+rate D <-> Y: 0.092966
+rate D <-> V: 0.034537
+rate C <-> Q: 0.327035
+rate C <-> E: 0.018914
+rate C <-> G: 0.601861
+rate C <-> H: 1.440267
+rate C <-> I: 0.884553
+rate C <-> L: 1.059394
+rate C <-> K: 0.075377
+rate C <-> M: 0.792828
+rate C <-> F: 1.802736
+rate C <-> P: 0.045666
+rate C <-> S: 2.482027
+rate C <-> T: 0.622941
+rate C <-> W: 1.244410
+rate C <-> Y: 3.667586
+rate C <-> V: 1.358909
+rate Q <-> E: 0.805150
+rate Q <-> G: 0.189236
+rate Q <-> H: 1.521058
+rate Q <-> I: 0.139356
+rate Q <-> L: 0.619366
+rate Q <-> K: 0.943418
+rate Q <-> M: 0.614987
+rate Q <-> F: 0.040291
+rate Q <-> P: 0.132287
+rate Q <-> S: 0.406615
+rate Q <-> T: 0.449516
+rate Q <-> W: 0.140722
+rate Q <-> Y: 0.094079
+rate Q <-> V: 0.244522
+rate E <-> G: 0.180515
+rate E <-> H: 0.110221
+rate E <-> I: 0.053530
+rate E <-> L: 0.051033
+rate E <-> K: 0.285935
+rate E <-> M: 0.081492
+rate E <-> F: 0.025491
+rate E <-> P: 0.086049
+rate E <-> S: 0.175210
+rate E <-> T: 0.232371
+rate E <-> W: 0.020451
+rate E <-> Y: 0.048931
+rate E <-> V: 0.247223
+rate G <-> H: 0.224620
+rate G <-> I: 0.006256
+rate G <-> L: 0.027163
+rate G <-> K: 0.125580
+rate G <-> M: 0.095029
+rate G <-> F: 0.064497
+rate G <-> P: 0.084826
+rate G <-> S: 1.181230
+rate G <-> T: 0.119971
+rate G <-> W: 0.179423
+rate G <-> Y: 0.019713
+rate G <-> V: 0.084795
+rate H <-> I: 0.188534
+rate H <-> L: 0.440029
+rate H <-> K: 0.234581
+rate H <-> M: 0.250508
+rate H <-> F: 1.251692
+rate H <-> P: 0.141588
+rate H <-> S: 0.421525
+rate H <-> T: 0.301567
+rate H <-> W: 0.414257
+rate H <-> Y: 4.345449
+rate H <-> V: 0.178237
+rate I <-> L: 2.144439
+rate I <-> K: 0.206102
+rate I <-> M: 3.009571
+rate I <-> F: 1.116368
+rate I <-> P: 0.021846
+rate I <-> S: 0.136478
+rate I <-> T: 1.677508
+rate I <-> W: 0.147934
+rate I <-> Y: 0.394337
+rate I <-> V: 7.490795
+rate L <-> K: 0.136907
+rate L <-> M: 4.424011
+rate L <-> F: 1.932758
+rate L <-> P: 0.146958
+rate L <-> S: 0.226771
+rate L <-> T: 0.218427
+rate L <-> W: 0.641257
+rate L <-> Y: 0.496820
+rate L <-> V: 1.130173
+rate K <-> M: 0.412932
+rate K <-> F: 0.031946
+rate K <-> P: 0.080652
+rate K <-> S: 0.269909
+rate K <-> T: 0.521119
+rate K <-> W: 0.032271
+rate K <-> Y: 0.052620
+rate K <-> V: 0.170515
+rate M <-> F: 1.521930
+rate M <-> P: 0.022195
+rate M <-> S: 0.190795
+rate M <-> T: 1.326117
+rate M <-> W: 0.649612
+rate M <-> Y: 0.500795
+rate M <-> V: 1.479391
+rate F <-> P: 0.047548
+rate F <-> S: 0.543810
+rate F <-> T: 0.178120
+rate F <-> W: 2.046607
+rate F <-> Y: 10.000000
+rate F <-> V: 0.637054
+rate P <-> S: 0.539321
+rate P <-> T: 0.162907
+rate P <-> W: 0.019994
+rate P <-> Y: 0.017689
+rate P <-> V: 0.139372
+rate S <-> T: 2.152037
+rate S <-> W: 0.187708
+rate S <-> Y: 0.277707
+rate S <-> V: 0.140613
+rate T <-> W: 0.087279
+rate T <-> Y: 0.118009
+rate T <-> V: 1.253591
+rate W <-> Y: 1.944524
+rate W <-> V: 0.122954
+rate Y <-> V: 0.324047
+
+freq pi(A): 0.104843
+freq pi(R): 0.078835
+freq pi(N): 0.043513
+freq pi(D): 0.090498
+freq pi(C): 0.002924
+freq pi(Q): 0.066163
+freq pi(E): 0.151640
+freq pi(G): 0.038843
+freq pi(H): 0.022556
+freq pi(I): 0.018383
+freq pi(L): 0.038687
+freq pi(K): 0.104462
+freq pi(M): 0.010166
+freq pi(F): 0.009089
+freq pi(P): 0.066950
+freq pi(S): 0.053667
+freq pi(T): 0.049486
+freq pi(W): 0.004409
+freq pi(Y): 0.012924
+freq pi(V): 0.031963
+
diff --git a/tests/misc/raxml_nucleotide.output b/tests/misc/raxml_nucleotide.output
new file mode 100644
index 0000000..214981f
--- /dev/null
+++ b/tests/misc/raxml_nucleotide.output
@@ -0,0 +1,66 @@
+
+
+This is RAxML version 7.3.9 released by Alexandros Stamatakis on November 8 2012.
+
+With greatly appreciated code contributions by:
+Andre Aberer (HITS)
+Simon Berger (HITS)
+Nick Pattengale (Sandia)
+Wayne Pfeiffer (SDSC)
+Akifumi S. Tanabe (Univ. Tsukuba)
+
+
+Alignment has 17 distinct alignment patterns
+
+Proportion of gaps and completely undetermined characters in this alignment: 0.00%
+
+RAxML Branch length scaler and other model parameter optimization up to an accuracy of 1.000000 log likelihood units
+
+Using 1 distinct models/data partitions with individual per partition branch length optimization
+
+
+All free model parameters will be estimated by RAxML
+GAMMA model of rate heteorgeneity, ML estimate of alpha-parameter
+
+GAMMA Model parameters will be estimated up to an accuracy of 1.0000000000 Log Likelihood units
+
+Partition: 0
+Alignment Patterns: 17
+Name: No Name Provided
+DataType: DNA
+Substitution Matrix: GTR
+
+
+
+
+RAxML was called as follows:
+
+/Users/Brett/Code/partitionfinder/programs/raxml -f B -s ./analysis/phyml/07a38f7681e0b117a187249439fd6c5d.phy -t ./analysis/start_tree/RAxML_result.BLTREE -m GTRGAMMA -n 07a38f7681e0b117a187249439fd6c5d_GTR+G.txt -w /Users/Brett/Code/partitionfinder/examples/nucleotide/analysis/phyml -e 1.0 -T 2 -O
+
+
+Likelihood: -405.660218
+
+
+Overall Time for Tree Evaluation with branch length scalers: 0.018874
+Final GAMMA likelihood: -405.660218
+
+Number of free parameters for AIC-TEST(BR-LEN): 10
+Number of free parameters for AIC-TEST(NO-BR-LEN): 9
+
+
+Model Parameters of Partition 0, Name: No Name Provided, Type of Data: DNA
+alpha: 2.933794
+Branch length scaler: 0.197764
+Tree-Length: 0.094369
+rate A <-> C: 3.202803
+rate A <-> G: 0.623071
+rate A <-> T: 0.220984
+rate C <-> G: 1.768328
+rate C <-> T: 0.000017
+rate G <-> T: 1.000000
+
+freq pi(A): 0.315909
+freq pi(C): 0.190909
+freq pi(G): 0.260227
+freq pi(T): 0.232955
+
diff --git a/tests/nuc_single_site/partition_finder.cfg b/tests/nuc_single_site/partition_finder.cfg
new file mode 100644
index 0000000..f3cbe97
--- /dev/null
+++ b/tests/nuc_single_site/partition_finder.cfg
@@ -0,0 +1,46 @@
+## ALIGNMENT FILE ##
+alignment = single_site.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = raxml;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = BIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+1 = 1;
+2 = 2;
+3 = 3;
+4 = 4;
+5 = 5;
+6 = 6;
+7 = 7;
+8 = 8;
+9 = 9;
+10 = 10;
+11 = 11;
+12 = 12;
+13 = 13;
+14 = 14;
+15 = 15;
+16 = 16;
+17 = 17;
+18 = 18;
+19 = 19;
+20 = 20;
+21 = 21;
+22 = 22;
+23 = 23;
+24 = 24;
+25 = 25;
+
+## SCHEMES, search: all | greedy | rcluster | hcluster | user | kmeans | kmeans_wss | kmeans_greedy ##
+[schemes]
+search = kmeans_greedy;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/nuc_single_site/single_site.phy b/tests/nuc_single_site/single_site.phy
new file mode 100644
index 0000000..6e3eb5d
--- /dev/null
+++ b/tests/nuc_single_site/single_site.phy
@@ -0,0 +1,33 @@
+32 25
+7 GTCAGACTGTCTGCATTGGACGACG
+14 GTCAGACTGTTTGCATTTAACGGTG
+1 ATCACATTGTATGCCTTTAACAGTC
+31 GTCCTATTTTTTGGTTTTTACAGTG
+16 GTTAAATTGTCTTGTTTTCCGAATG
+20 GTCAAATTGTCATGTTTTTAGACTG
+19 GTCAGATTGTCAAGTTTTTAGAGAG
+28 GTTAAATCGTAAAGTTTTTCGACTG
+22 GTTAAACCGTAAAGTTTTTCGACTG
+15 GTTAAACCGCAAAGTTTTTCGAATG
+18 GTTACAACGCGAAGTTTTTCGAGTG
+17 GTCAGCCTATTTGCATTAAACAGTG
+29 GTGAGCCTGTTCGCATTAACCAGCG
+12 GTCATCTTGTTCGCACTTAACAGTA
+2 GTCATCTTGTTCGCCTAAAACAGGA
+26 GTCGTCTTGTTAGTTTAAAACAGGA
+32 GTCAGATTGTTTAGATTGAACGGTG
+30 GTCAGTTTGTTTACATTGAACGGCC
+9 GTTAGATTGTTTACATTGAGCGCCA
+3 GATATATGGTTTACCTTGAGCGGCA
+13 AATATATGGTTTACGTTGCGCAGAA
+25 AATATATCGTTTACGTTGAGCAGCA
+24 GTTAGACAGCTTACCTTTCGCAATG
+23 GTCAGACTGTTAGCAATTCGCATTG
+4 GTTCGACCGTGCGCAATTAGCATTG
+11 GTAACACTGTGTGCAATTAGCATTG
+21 CTATCACTTGATGCAATTAGCATTG
+8 GCTTTACTCGATACAATTAGCATAG
+10 CCATTGCTCAATACAAATCTCATCG
+27 ACATTACTCGATACAATTATCATCG
+5 CCATGACGATATAGAATTCTCATCG
+6 GCATTACTAGATAGAATTATCACCG
diff --git a/tests/paul/RAxML_perSiteLLs.testing b/tests/paul/RAxML_perSiteLLs.testing
new file mode 100644
index 0000000..8d4115d
--- /dev/null
+++ b/tests/paul/RAxML_perSiteLLs.testing
@@ -0,0 +1,2 @@
+ 1 10
+tr1 -2.705940 -2.705940 -2.698479 -5.225005 -2.714398 -2.698479 -2.705940 -2.705940 -2.705940 -5.255713
diff --git a/tests/paul/__init__.py b/tests/paul/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/paul/fabricated/fabricated.phy b/tests/paul/fabricated/fabricated.phy
new file mode 100644
index 0000000..0f846b2
--- /dev/null
+++ b/tests/paul/fabricated/fabricated.phy
@@ -0,0 +1,11 @@
+10 305
+1 AAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAATTTTT-----
+2 -AAAA-TTTT-CCCC-GGGG-AAAATTTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-----
+3 A-AAAT-TTTC-CCCG-GGGA-AAATTTTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTTA-AAAT-TTTC-CCCG-GGGA-AAAT-TTT-----
+4 AA-AATT-TTCC-CCGG-GGAA-AATTTTTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TTAA-AATT-TTCC-CCGG-GGAA-AATT-TT-----
+5 AAA-ATTT-TCCC-CGGG-GAAA-ATTTTTAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-TAAA-ATTT-TCCC-CGGG-GAAA-ATTT-T-----
+6 AAAA-TTTT-CCCC-GGGG-AAAA-TTTTTAAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT-AAAA-TTTT-CCCC-GGGG-AAAA-TTTT------
+7 AAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGGAAAAATTTTTCCCCCGGGGGAAAAAGGGGG-----
+8 AAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCCAAAAATTTTTCCCCCGGGGGAAAAACCCCC-----
+9 AAAAATTTTTCCCCCGGGGGAAAAATTTTTAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAAAAAAATTTTTCCCCCGGGGGAAAAAAAAAA-----
+10 AAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTTAAAAATTTTTCCCCC-----AAAAATTTTT-----
diff --git a/tests/paul/fabricated/partition_finder.cfg b/tests/paul/fabricated/partition_finder.cfg
new file mode 100644
index 0000000..ba35f52
--- /dev/null
+++ b/tests/paul/fabricated/partition_finder.cfg
@@ -0,0 +1,34 @@
+## ALIGNMENT FILE ##
+alignment = fabricated.phy;
+
+## BRANCHLENGTHS: linked | unlinked ##
+branchlengths = linked;
+
+## MODELS OF EVOLUTION for PartitionFinder: all | raxml | mrbayes | beast | <list> ##
+## for PartitionFinderProtein: all_protein | <list> ##
+models = GTR+G;
+
+# MODEL SELECCTION: AIC | AICc | BIC #
+model_selection = AIC;
+
+## DATA BLOCKS: see manual for how to define ##
+[data_blocks]
+## Gene1 = 1-789; ##
+## Gene1_pos1 = 1-789\3; ##
+## Gene1_pos2 = 2-789\3; ##
+## Gene1_pos3 = 3-789\3; ##
+## Gene2 = 790-1449; ##
+## Gene2_pos1 = 790-1449\3; ##
+## Gene2_pos2 = 791-1449\3; ##
+## Gene2_pos3 = 792-1449\3; ##
+## Gene3 = 1450-2208; ##
+## Gene3_pos1 = 1450-2208\3; ##
+## Gene3_pos2 = 1451-2208\3; ##
+## Gene3_pos3 = 1452-2208\3; ##
+All = 1-305;
+
+## SCHEMES, search: all | greedy | rcluster | hcluster | user | kmeans | kmeans_wss | kmeans_greedy ##
+[schemes]
+search = kmeans;
+
+#user schemes go here if search=user. See manual for how to define.#
diff --git a/tests/paul/free_rates_4_cat.phy_phyml_lk.txt b/tests/paul/free_rates_4_cat.phy_phyml_lk.txt
new file mode 100644
index 0000000..8b43dca
--- /dev/null
+++ b/tests/paul/free_rates_4_cat.phy_phyml_lk.txt
@@ -0,0 +1,17 @@
+Note : P(D|M) is the probability of site D given the model M (i.e., the site likelihood)
+P(D|M,rr[x]) is the probability of site D given the model M and the relative rate
+of evolution rr[x], where x is the class of rate to be considered.
+We have P(D|M) = \sum_x P(x) x P(D|M,rr[x]).
+
+
+Site P(D|M) P(D|M,rr[1]=2.6534) P(D|M,rr[2]=0.2289) P(D|M,rr[3]=0.4957) P(D|M,rr[4]=1.0697) Posterior mean
+1 2.07027e-12 1.3895e-19 6.2676e-12 1.2534e-12 1.21786e-15 0.273422
+2 1.8652e-07 2.05811e-19 6.73481e-07 4.14575e-09 7.97623e-14 0.23049
+3 4.48873e-15 1.37274e-19 7.11221e-15 9.11826e-15 9.21848e-17 0.382265
+4 3.38958e-10 1.31413e-19 1.18939e-09 4.20659e-11 5.86537e-15 0.237972
+5 8.29969e-17 1.11587e-19 3.1672e-17 2.52183e-16 1.9722e-17 0.502077
+6 9.24579e-09 1.59891e-19 3.31101e-08 4.79946e-10 2.59524e-14 0.232669
+7 3.43996e-10 2.1917e-19 1.19544e-09 5.43128e-11 1.22969e-14 0.240455
+8 4.43262e-13 1.1447e-19 1.32148e-12 2.8874e-13 3.7386e-16 0.27685
+9 3.42513e-11 1.70149e-19 1.14227e-10 1.02103e-11 4.05239e-15 0.250765
+10 1.15506e-11 1.28107e-19 3.86378e-11 3.32642e-12 1.46151e-15 0.250024
diff --git a/tests/paul/gamma_8_cat.phy_phyml_lk.txt b/tests/paul/gamma_8_cat.phy_phyml_lk.txt
new file mode 100644
index 0000000..5ff3010
--- /dev/null
+++ b/tests/paul/gamma_8_cat.phy_phyml_lk.txt
@@ -0,0 +1,17 @@
+Note : P(D|M) is the probability of site D given the model M (i.e., the site likelihood)
+P(D|M,rr[x]) is the probability of site D given the model M and the relative rate
+of evolution rr[x], where x is the class of rate to be considered.
+We have P(D|M) = \sum_x P(x) x P(D|M,rr[x]).
+
+
+Site P(D|M) P(D|M,rr[1]=0.1728) P(D|M,rr[2]=0.3657) P(D|M,rr[3]=0.5439) P(D|M,rr[4]=0.7331) P(D|M,rr[5]=0.9506) P(D|M,rr[6]=1.2228) P(D|M,rr[7]=1.6122) P(D|M,rr[8]=2.3989) Posterior mean
+1 1.36373e-12 3.60785e-12 5.44944e-12 1.58289e-12 2.45474e-13 2.29162e-14 1.22494e-15 3.35077e-17 4.90601e-19 0.33735
+2 2.87895e-07 2.16944e-06 1.27515e-07 5.98776e-09 2.18854e-10 5.42051e-12 7.49452e-14 4.51885e-16 1.18074e-18 0.184513
+3 3.67318e-15 1.63466e-15 1.32314e-14 1.01795e-14 3.5268e-15 7.16337e-16 8.94944e-17 6.8864e-18 3.49039e-19 0.477974
+4 2.75073e-10 1.64216e-09 4.95499e-10 5.82998e-11 4.41172e-12 2.1336e-13 5.88679e-15 7.95885e-17 5.64329e-19 0.227273
+5 8.1444e-17 2.82279e-18 1.22459e-16 2.45719e-16 1.83404e-16 7.52518e-17 1.87904e-17 2.85338e-18 2.52601e-19 0.634017
+6 9.90893e-09 6.94317e-08 9.12817e-09 6.74745e-10 3.55841e-11 1.25053e-12 2.52239e-14 2.34373e-16 8.81134e-19 0.198446
+7 2.54015e-10 1.44787e-09 5.08831e-10 6.89929e-11 6.06564e-12 3.4634e-13 1.14327e-14 1.77155e-16 1.07488e-18 0.235515
+8 3.07761e-13 7.83485e-13 1.23463e-12 3.7553e-13 6.17754e-14 6.26968e-15 3.81829e-16 1.31831e-17 3.20361e-19 0.342335
+9 2.23513e-11 9.637e-11 6.79003e-11 1.29863e-11 1.44982e-12 1.00113e-13 3.93728e-15 7.65775e-17 7.18937e-19 0.278002
+10 7.8803e-12 3.47616e-11 2.33762e-11 4.37891e-12 4.89457e-13 3.47469e-14 1.45604e-15 3.20495e-17 4.30831e-19 0.274906
\ No newline at end of file
diff --git a/tests/paul/simulated_TRUE.phy_phyml_lk.txt b/tests/paul/simulated_TRUE.phy_phyml_lk.txt
new file mode 100644
index 0000000..45e2a95
--- /dev/null
+++ b/tests/paul/simulated_TRUE.phy_phyml_lk.txt
@@ -0,0 +1,14 @@
+Note : P(D|M) is the probability of site D given the model M (i.e., the site likelihood)
+
+
+Site P(D|M)
+1 0.0565097
+2 0.0565097
+3 0.0580009
+4 0.00728218
+5 0.0569829
+6 0.0580009
+7 0.0565097
+8 0.0565097
+9 0.0565097
+10 0.00722309
\ No newline at end of file
diff --git a/tests/quick_analysis/__init__.py b/tests/quick_analysis/__init__.py
new file mode 100644
index 0000000..e69de29
diff --git a/tests/quick_analysis/all/partition_finder.cfg b/tests/quick_analysis/all/partition_finder.cfg
new file mode 100644
index 0000000..25dba1a
--- /dev/null
+++ b/tests/quick_analysis/all/partition_finder.cfg
@@ -0,0 +1,32 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = all;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
diff --git a/tests/quick_analysis/all/random.phy b/tests/quick_analysis/all/random.phy
new file mode 100644
index 0000000..b4e17fa
--- /dev/null
+++ b/tests/quick_analysis/all/random.phy
@@ -0,0 +1,7 @@
+5 100
+
+spp1 actgactgaaaactgatcgatcgatcgatgctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagactagctagc
+spp2 tctgtctgttttttgttcgttcgttcgttgctttcttgctttcttgctttcttgcttgcttgcttgcttgcttgcttgcttgcttgcttgtcttgcttgc
+spp3 agtgagtgaaaagtgatggatggatggatggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtagagtaggtagg
+spp4 actaactaaaaactaatcaatcaatcaatactaactaactaactaactaactaactaactaactaactaactaactaactaactaactaaactaactaac
+spp5 acagacagaaaacagaacgaacgaacgaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagacaagcaagc
diff --git a/tests/quick_analysis/aln_RY/partition_finder.cfg b/tests/quick_analysis/aln_RY/partition_finder.cfg
new file mode 100644
index 0000000..ce9a74d
--- /dev/null
+++ b/tests/quick_analysis/aln_RY/partition_finder.cfg
@@ -0,0 +1,36 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+s1 = (p1, p2, p3, p4, p5);
+s2 = (p1, p2) (p3, p4, p5);
+s3 = (p1, p2) (p3) (p4, p5);
+s4 = (p1, p5) (p3, p4) (p2);
diff --git a/tests/quick_analysis/aln_RY/random.phy b/tests/quick_analysis/aln_RY/random.phy
new file mode 100644
index 0000000..8413bda
--- /dev/null
+++ b/tests/quick_analysis/aln_RY/random.phy
@@ -0,0 +1,132 @@
+10 705
+Row YRYYRYRYRRRRYRYRYYRRYYYYRRRRYYYYRYRYYRYRRYRRYYRRYRYYYYYYYRRY
+Rarp YRYYRYRYRRRYYRYRYYRRYYYRRRRYYYYYRYRYYRRYRYRRRYRRYRYYYYYYYRRR
+Rhicken YRYYRRYYRRYRRRRRYYRRYYYRRRRRYYYYRYRRRRYRRRRRRYRRYRYYYYYYYRRR
+Human YRYYRYRYRYRYYRYRYYYRYYYRRRYRYYYYRYRRYRRRRRRRRYRRYRYYYYYYYRRR
+Loach YRYYRYRYRRRRYRYRYYRRYYYYRRRRYYYYRYRYYRRRRYRRRYRYYRYYYYYYYRRR
+Mouse YRYYRRRYRRRYRRRRYYRRRYYRRRYRYYYYRYRRYRYRRRRRRYRRYRYYYYYYYRRY
+Rat YRYYRRRYRRRYRRRRYYRRRYYRRRYRYYYYRYRRYRYRRYRRRYRRYRYYYYYYYRRR
+Seal YRYYRYRYRRRRRRYRYYYRYYYRRRYRYYYYRYRYYRRRRRRRRYRRYRYYYYYYYRRY
+Whale YRYYRYRYRRRYRRRRYYRRYYYRRRRRYYYYRYRYYRYRRYRRRYRRYRYYYYYYYRRR
+Frog YRYYRYRYRRRYRRYRYYRRYYYRRRRRYYYYRYRYYRRRRRRRYYRRYRYYYYYYYRRY
+
+RRRRYRRRRRYRYYRRYRYRYRRYYRYYRRYRRRRRRRYYRRYYRRRYRRYYRYRRRRYR
+RRRRYRRRRRYRYYRRYRYRYRRYYRYYRRYRYRRRRRYYRRYYRYRRRRYYRRRRYRYR
+YRRYYYRRRRYRYYRRYRYRRRRYYRYYRRYRYRRYYRYYRRRYRYYRRRYYRYRRRRYR
+YRRYRRRRRRYRYYRRYRYRRRRRYRYYRRYRRRRRRRRYRRRYRRRRRRYYRRRRYRYR
+RRRRYRRRRRYRYYRRYRYRRRRYYRYYRRYRYRRRRRYYRRYYRYRRRRYYRYRRRRYR
+YRYYYRRRRRYRYYRRYRYRYRRYYRYYRRYRRRRRRRYYRRYYRRRRRRYYRRRRRRYR
+YRYYYRRRRRYRYYRRYRYRRRRYYRYYRRYRYRRRRRRYRRYYRRRRRRYYRYRRRRYR
+RRYRYRRRRRYRYYRRYRYRYRRYYRYYRRYRYRRRRRYYRRYYRRRYRRYYRYRRRRYR
+RRYRYRRRRRYRYYRRYRYRYRRYYRYYRRYRRRRRRRYYRRYYRRRRRRYYRRRRRRYR
+RRRRYRRRRRYRYYRRYRYRRRRRYRYYRRYRRRRRRRRYRRYYRYRYRRYYRRRRRRYR
+
+YRRYRRRRYRRYYRYRRYYRYYRYYYYRRYYRRRYRYRYYYRYRYYRYYYRYRYRYYYYY
+YRRYRRYRRYRYYRYYRYRRYYRRYYYRRRYRRYYRYYYRYRYRRRRYYYRRRRRYYYYY
+RRRRRYYRRRRRYRYRRRYRYYYYYYYRRYRRY---RRYYYRYRRYRYYYRYRRRYYYYY
+YRRRRRRRRRRYYRYRRRYRYYRYYYYRRYYRRYYRYRRYYRYRRRRYYYRYRRRYYYYY
+YRRYRRYRRYRYYRRYRRRRYYRYYYYRRRYRRYYRYRYRYRYRRRRYYYRRRYRYYYYY
+YRRYRRRRYRRYYRYRRYYRYYRYYYYRRYYRYRYRYRYYYRYRYYRYYYRYRYRYYYYY
+YRRYRRRRYRRYYRYRRYYRYYRYYYYRRYYRYRYRYRYYYRYRYYRYYYRYRRRYYYYY
+YRRYRRRRYRRRYRYRRYYRRYRYYYYRRRYRRRYRYRYYYRYRYYRYYYRYRYRYYYYY
+YRRYRRYRRRRYYRYRRRYRYYRRYYYRRYYRYRYRYRRYYRYRYYRYYYRYRRRYYYYY
+YRRYRRYRRYRRYRYYRYYRRYRRYYYRRYYRRYYRYRYYYRRRYYRYYYRYRYRYYYYY
+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+RRYRYYYRRRRYRYRYRYYRYYYRYYYYRRYYRYYRRRYRRRRRRYRYYRYYYYYRRYRY
+RRYRYRYRRRRYRYRRRRYRYYYRYYYYRRYYRYYRRRRRYRRRYYRYYRRYYYYRYYRY
+RRRRYYYRRRRRRYRYRYYRYYYRYYYYRRYYRYYYRRRYYRRRRYRRRRYYYYYRRYRR
+RRYRYRYRRRRRRYRYRYYRYYYRYYYYRRYYRYYRRRRRRRRRRYRRYRRYYYRRYYRR
+RRYRYYYRRRRYRYRRRRYRYYYRYYYYRRYYRYYRRRRRYRRRYYRYYRRYYYYRRYRY
+RRYRYRYRRRRYRYRYRYYRYYYRYYYYRRYYRYYRRRRYRYRRYYRRYRRYYYYRRYRY
+RRYRYYYRRRRYRYRYRYYRYYYRYYYYRRYYRYYRRRYYRRRRYYRYYRYYYYYRRYRY
+RRYRYYYRRRRRRYRYRYYRYYYRYYYYRRYYRYYRRRRRRRRRYYRRYRYYYYYRRYRY
+RRYRYYYRRRRRRYRYRYYRYYYRYYYYRRYYRYYRRRRRRRRRRYRRYRYYYYYRYYRY
+RRRRYRYRRRRYRYRRRYYRYYYRYYYYRRYYRYYRRRYRYRRRYYRYYRRYYYYRYYRR
+
+YYYRYRRYYRYYRYRRYYYYRRYRYYYRYRYRYYYRRYRYYYYYRRRYYYRRRRYYRRRR
+YYYRYRRYYRYYRYRRYYYYRRYRYYYRYRYRYYYRRYRYYYYYRRRYYYYRRRYYRRRR
+YYYRYRRYYRYYRYRRYYYRRRYRYYYRYRYRYYYRRRRYYYYYRRRRRRYRRRYYRRRR
+YYRRYRRYYRYYRYRRYYYRRRYRYYYRYRYRRYYRRYRYYRYYYRRYYRRRRRYYRRRR
+YYYRYRRYYRYYRYRRYYYYRRYRYYYRYRYRRYYRRYRYYYYYRRRYYYRRRRYYRRRR
+YYYRYRRYYRYYRYRRYYYYRRYRYYYRYRYRRYYRRYRYYYYYRRRYRYRRRRYYRRRY
+YYYRYRRYYRYYRYRRYYYYRRYRYYYRYRYRRYYRRYRYYYYYRRRYRYRRRRYYRRRR
+YYYRYRRYYRYYRYRRYYYYRRYRYYYRYRYRYYYRRYRYYYYYRRRYYYRRRRYYRRRY
+YYRRYRRYYRYYRYRRYYYYRRYRYYYRYRYRRYYRRYRYYYYYRRRYYYRRRRYYRRRR
+YYRRYRRYYRYYRYRRYYYYRRYRYYYRYRYRRYYRRYRYYYYYRRRRRRYRRRYYRRRR
+
+RYRYRYYRRRRYYRYRRYYYYRRYYYYRRYYYYYYYRRYRYYRRYRRYYYYYRRYYRYYR
+RYRYRYYRYRRYYRRRYYYYRRRRYRRRRRYYYRYYRRRRYYRRRRRYYYYYRYYYRRYR
+RYRYRYYRRRRYYRYYRYYYRRRRRRRRRYYYRRYRRRRRYRRRYRRYYYYYRRYYRRYR
+RYRYRYRRRRRRRRYRRYRRRRRYYYYRRYYYRYYRRRYRYYRRRRRRYYRYRRYYRYYR
+RYRYRYYRRRRRYRRRYYYYRRRYYRRRRRYYYRYYRRRRYYRRYRRYYYYYRYYYRRYR
+RYRYRYYRRRRYYRYYYRYYRRRYYYYRRRYYRYYYRRYRYYRRYRRYYYYYRRYYRYYR
+RYRYRYYRRRRYYRRYYRYYRRRYYYYRRYYYRYYYRRRRYRRRYRRYYYYYRRYYRYYR
+RYRYRYYRRRRRYRYRYYYYYRRYYYYRRRYYYYYYRRYRYYRRYRRYYYYYRYYYRYYR
+RYRYRYYRRRRYYRYRRYYYRRRYYYYRRYYYYYYYRRYRYYRRYRRYYYYYRYYYRYYR
+RYRYRYYRRRRYYRRYYRYYRRRRYRRRRRYYYRYYRRRRYYRRYRRYYYYYRRYYRYYR
+
+RYYYRRYRYRRYRRYYRYYYYYRYYRYYRRRYYYRYRRYYRRRRRRRRYYYYYRYRYRRY
+RYYYRYYRRYRRRRYYRYYYYRRRRRYYRRRYRYRRRRYYRYRRRYRRYYYYYRYRYRRY
+RYRYRRYRYYRRRRRYRYYYYRRRRRRYRRRYYYRYYRRYRRYRRYRRYYRYYRYRRRRR
+RYYYRYYRYRRRRRYYRRYYYYRRRRRYRRRYRYRYYRYYRRYRYRRYRYYYYRYRRRRY
+RYYYRYYRRYRRRRRYRYYYYRRRRRRYRRRYRYRRRRRYRRRRRYRRYYYYYRYRYRRY
+RYYYRRYRRRRYRRYYRYYYYRRRRRYYRRRYRYRYRRYYRRRRYRRRYYYYYRYRRRRR
+RYYYRYYRRRRYRRYYRYYYYRRRRRYYRRRYRYRYRRYYRRRRYRRRYYYYYRYRRRRY
+RYYYRYYRRRRRRRYYRYYYYYRYYRYYRRRYRYRYRRYYRRRRYRRYYYYYYRYRYRRR
+RYYYRRYRRRRYRRRYRYYYYYRYYRYYRRRYYYRYRRYYRRRRYRRYYYYYYRYRYRRR
+RYYYRYYRYYRRRRYYRYYYYRRRRRYYRRRYYRRRRRYYRRYRYYRRYYYYYRYRRRRR
+
+RYRRRYRYYYRRYRYRRRRRRRRYYYYRRYYYYYRYYYRYRYYRRRRYYYRRYRRRYYYR
+RYRRRRRYYYRRYRRRRYRRRRRRYYRYRYYYYYRYYYRYRYYRRRRYYYYRYYRRYYYR
+RYRRRYRYYYRRYRYRRRYRRRRRYYYYRYYYYYRYYYRYRYYRRRRRYYYRYYRRYYYR
+RYRRRYRYYYRRYRRRRRYRYRRYYYRRRYYYYYRYYYRYRYYRRRRRYYYRYRRRYYYR
+RYRRRRRYYYRRRRRRRYYRRYRYYYYYRYYYYYRYYYRYRYYRRRRYYYYRYRRRRYYR
+RYRRRYRYYYRYYRRRRRRRRRRYYYYRRRYYYYRRYYRYRRYRRRRYYYRRYYRRYYYR
+RYRRRYRYYYRRYRRRRRRRYRRYYYYRRYYYYYRRYYRYRYYRRRRRYYRRYRRRYYYR
+RYRRRYRYYYRRYRYRRYRRRRRYYYYRRYYYYYRRYYRYRRYRRRRYYYYRYYRRYYYR
+RYRRRYRYYYRRYRYRRRRRRRRYYYRRRYYYYYRYYYRYRYYRRRRYYYYRYRRRYYYR
+RYRRRYRYYYRRYRYRRRRRRRRYYYRYRRYYYYRYYYRYRYYRRRRYYYYRYYRRRRYR
+
+RYYYRYYRRRRRYRYRRYRRRRYRRRYYYRRRYRYRRYRYYRRYYRYRRRYYYYYRRRYR
+RYYYRRYRRRRRYRRYRRRRYRYRRRYYYYYRRRRRRYRYYYRYYRYRRRRYYYYRRRYR
+RYYYRRRRRRRRYRRYRRYRRRYYRRYYYYYRYRRRRYRYYYRYYRYRRRYYYYYRRRYR
+RYYYRRYRRRRRYRRYRRYRYRYYRRYYYYYRYRYRRYRYYRRYYRYRRRRYYYYRRRYR
+RYYYRRYRRRRRYRRYRRRRRRYRRRRYYYYRYRRRRYRYYYRYYRYRRRYYYYYRRRYR
+RYYYRYYRYYRYYRYRRYYYRRYYRRYYYYRRYRRRRYRYYRRYYRYRRRRYYYYRRRYR
+RYYYRRYRYYRRYRYRRYYYRRYYRRYYYRRRYRRRRYRYYRRYYRYRRRRYYYYRRRYR
+RYYYRYYRRRRYYRYYRRYRYRYYRRYYYYRRYRYRRYRYYRRYYRYRRRYYYYYRRRYR
+RYYYRYYRRRRYYRYRRYYRYRYYRRYYYRRRYRRRRYRYYYRYYRYRRRYYYYYRRRYR
+RYYYRYRRYRRRYRRYRRYRRRYRRRYYYYYRYRRRRYRYYYRYYRYRRRYYYYYRRRYR
+
+YYYRRYYYRRYRYYRRRRYRYRRRYRRYRRRRRYYYRRYYRRRRYRRYYYYRYRRRRYYY
+YYYYRRYYRRYRYYRRRRYRYRRYYRRYRYYRRYYYYRYYRYRRRRRRYYYRYRRRRYYY
+YYYYRRYYRRYRYYRRYRYRYRRRYRRYRYYRYYYYRRRYRRRRRRRYYYYRYRRRRYYY
+YYYYRYYYRRYRYYRRRRYRYRRRYRRYRRRRYYYYRRYYRRRRRRRYYYYYRRRRRYYY
+YYYYRYYYRRYRYYRRRRYRYRRRYRRYRYYRYYYYYRYYRRRRYRRYRRRRYRRRRYYY
+YYYRRRYYRRYRYYRRRRYRYRRRYRRYRRRRYYYYYRYYRRRRYRRYYYYRYRRRRYYY
+YYRRRYYYRRYRYYRRRRYRYRRRYRRYRYRRYYYYYRYYRYRRRRRYYYYRYRRRRYYY
+YYRRRYYYRRYRYYRRRRYRYRRRYRRYRRRRRYYYRRYYRRRRYRRYRRRRYRRRRYYY
+YYRRRYYYRRYRYYRRRRYRYRRYYRRYRRRRYYYYRRYYRYRRRRRYYYYYRRRRRYYY
+YYYYRYYYRRYRYYRRRRYRYRRYYRRYRYYRRYYYYRYYRYRRYRRYYRRYYRRRRYYY
+
+YYYRYYRRRYRYRRYYRYRRY---------------------RYY
+YYRRYYRRRRRYRRYYRYRRYYYYYYRYRRRRYRRYYYYYYRRYY
+YRRRYYRRRRRYRRY------------------RRYRRYRRRRYY
+YRY---------------------YYYRRRYRYRRRYRRRRYRYY
+YYRRYYRRRYRRRRRYRYRRYYYYYYRYRRRRYRRYYYYYYRRYY
+YYRRYYRRRYRRRRYYRYYRR---------------------RYY
+YYRRYYRRYYRRRRRYRYYRR---------------------RYY
+YYYRYYRRRYRRRRYYRYRRR---------------------RYY
+YYYRYYRRRYRYRRYYRYRRY---------------------RYY
+YYRRYYRRRRRYRRYYRYRRY---YYYYRYRRYRRY------YYY
\ No newline at end of file
diff --git a/tests/quick_analysis/aln_interleaved/partition_finder.cfg b/tests/quick_analysis/aln_interleaved/partition_finder.cfg
new file mode 100644
index 0000000..ce9a74d
--- /dev/null
+++ b/tests/quick_analysis/aln_interleaved/partition_finder.cfg
@@ -0,0 +1,36 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+s1 = (p1, p2, p3, p4, p5);
+s2 = (p1, p2) (p3, p4, p5);
+s3 = (p1, p2) (p3) (p4, p5);
+s4 = (p1, p5) (p3, p4) (p2);
diff --git a/tests/quick_analysis/aln_interleaved/random.phy b/tests/quick_analysis/aln_interleaved/random.phy
new file mode 100644
index 0000000..818010b
--- /dev/null
+++ b/tests/quick_analysis/aln_interleaved/random.phy
@@ -0,0 +1,132 @@
+10 705
+Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA
+Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT
+Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC
+Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT
+Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT
+Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA
+Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT
+Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA
+Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC
+Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA
+
+CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC
+CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT
+GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC
+ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT
+CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT
+ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT
+ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT
+CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC
+CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC
+CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC
+
+ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA
+ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA
+CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA
+GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA
+GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA
+ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA
+ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA
+ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA
+ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA
+ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG
+
+GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT
+ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC
+GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC
+ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC
+ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA
+GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT
+GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC
+GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA
+GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA
+ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC
+
+TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA
+CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA
+CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC
+CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT
+CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG
+CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA
+CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA
+TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA
+TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA
+CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC
+
+GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC
+GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC
+GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC
+GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC
+GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC
+GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA
+GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC
+GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA
+GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC
+GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT
+
+TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT
+TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC
+TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT
+TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT
+TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC
+TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC
+TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT
+TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT
+TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC
+TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT
+
+CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA
+CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA
+CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC
+CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG
+CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA
+CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC
+CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG
+CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC
+CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC
+CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC
+
+CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC
+CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT
+CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT
+CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC
+CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC
+CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT
+CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC
+CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC
+CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC
+CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT
+
+CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC
+CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT
+CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC
+CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT
+CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT
+CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT
+CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC
+CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT
+CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC
+CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC
+
+GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA
+GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA
+GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA
+GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA
+GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA
+GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA
+GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA
+GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG
+GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA
+GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA
+
+AAATGATCTGCGTCAATATTA---------------------TAA
+AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA
+GCCTGATCCTCACTA------------------CTGTCATCTTAA
+ATA---------------------GGGCCCGTATTTACCCTATAG
+AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA
+AACTGATCTGCTTCAATAATT---------------------TAA
+AACTGATCAGCTTCTATAATT---------------------TAA
+AAATGATCTACCTCAATGCTT---------------------TAA
+AAATGATCTGTATCAATACTA---------------------TAA
+AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA
\ No newline at end of file
diff --git a/tests/quick_analysis/greedy/partition_finder.cfg b/tests/quick_analysis/greedy/partition_finder.cfg
new file mode 100644
index 0000000..7ed9d1e
--- /dev/null
+++ b/tests/quick_analysis/greedy/partition_finder.cfg
@@ -0,0 +1,32 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = greedy;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
diff --git a/tests/quick_analysis/greedy/random.phy b/tests/quick_analysis/greedy/random.phy
new file mode 100644
index 0000000..b4e17fa
--- /dev/null
+++ b/tests/quick_analysis/greedy/random.phy
@@ -0,0 +1,7 @@
+5 100
+
+spp1 actgactgaaaactgatcgatcgatcgatgctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagactagctagc
+spp2 tctgtctgttttttgttcgttcgttcgttgctttcttgctttcttgctttcttgcttgcttgcttgcttgcttgcttgcttgcttgcttgtcttgcttgc
+spp3 agtgagtgaaaagtgatggatggatggatggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtagagtaggtagg
+spp4 actaactaaaaactaatcaatcaatcaatactaactaactaactaactaactaactaactaactaactaactaactaactaactaactaaactaactaac
+spp5 acagacagaaaacagaacgaacgaacgaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagacaagcaagc
diff --git a/tests/quick_analysis/maclinebreaks/partition_finder.cfg b/tests/quick_analysis/maclinebreaks/partition_finder.cfg
new file mode 100644
index 0000000..7ca6374
--- /dev/null
+++ b/tests/quick_analysis/maclinebreaks/partition_finder.cfg
@@ -0,0 +1 @@
+#NB Don't forget the semi-colons at the end of every statement!
## ALIGNMENT FILE ##
# the name of your phylip alignment
alignment = random.phy;
## BRANCHLENGTHS ##
# 'linked' or 'unlinked'. Most people will want 'linked'
branchlengths = linked;
## MODELS OF EVOLUTION ##
# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
models = GTR;
# model selection: 'AIC', 'AICc', or 'BIC'
model_selection = BIC;
## PARTITIONS ##
# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
[data_blocks]
p1 = 1-20;
p2 = 21-40;
p3 = 41-60;
p4 = 61-80;
p5 = 81-100;
## SCHEMES ##
# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
[schemes]
search = user;
#user schemes. Only used if 'search = user'. See manual for how to define.
s1 = (p1, p2, p3, p4, p5);
s2 = (p1, p2) (p3, p4, p5);
s3 = (p1, p2) (p3) (p4, p5);
s4 = (p1, p5) (p3, p4) (p2);
\ No newline at end of file
diff --git a/tests/quick_analysis/maclinebreaks/random.phy b/tests/quick_analysis/maclinebreaks/random.phy
new file mode 100644
index 0000000..037dff6
--- /dev/null
+++ b/tests/quick_analysis/maclinebreaks/random.phy
@@ -0,0 +1 @@
+5 100
spp1 actgactgaaaactgatcgatcgatcgatgctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagactagctagc
spp2 tctgtctgttttttgttcgttcgttcgttgctttcttgctttcttgctttcttgcttgcttgcttgcttgcttgcttgcttgcttgcttgtcttgcttgc
spp3 agtgagtgaaaagtgatggatggatggatggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtagagtaggtagg
spp4 actaactaaaaactaatcaatcaatcaatactaactaactaactaactaactaactaactaactaactaactaactaactaactaactaaactaactaac
spp5 acagacagaaaacagaacgaacgaacgaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagacaagcaagc
\ No newline at end of file
diff --git a/tests/quick_analysis/test_quick.py b/tests/quick_analysis/test_quick.py
new file mode 100644
index 0000000..9b9632a
--- /dev/null
+++ b/tests/quick_analysis/test_quick.py
@@ -0,0 +1,27 @@
+import os
+from partfinder import main
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+
+
+def get_test_folders():
+ testdirs = []
+ # Get everything that is here...
+ for p in os.listdir(HERE):
+ if p.startswith('__'):
+ continue
+ d = os.path.join(HERE, p)
+ if os.path.isdir(d):
+ testdirs.append(p)
+ return testdirs
+
+
+def pytest_generate_tests(metafunc):
+ # This function feeds the output of the above function into the tests below
+ if 'test_folder' in metafunc.fixturenames:
+ metafunc.parametrize("test_folder", get_test_folders())
+
+
+def test_quick_analysis(test_folder):
+ full_path = os.path.join(HERE, test_folder)
+ main.call_main("DNA", '"%s" --force-restart' % full_path)
diff --git a/tests/quick_analysis/user/partition_finder.cfg b/tests/quick_analysis/user/partition_finder.cfg
new file mode 100644
index 0000000..ce9a74d
--- /dev/null
+++ b/tests/quick_analysis/user/partition_finder.cfg
@@ -0,0 +1,36 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+s1 = (p1, p2, p3, p4, p5);
+s2 = (p1, p2) (p3, p4, p5);
+s3 = (p1, p2) (p3) (p4, p5);
+s4 = (p1, p5) (p3, p4) (p2);
diff --git a/tests/quick_analysis/user/random.phy b/tests/quick_analysis/user/random.phy
new file mode 100644
index 0000000..b4e17fa
--- /dev/null
+++ b/tests/quick_analysis/user/random.phy
@@ -0,0 +1,7 @@
+5 100
+
+spp1 actgactgaaaactgatcgatcgatcgatgctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagactagctagc
+spp2 tctgtctgttttttgttcgttcgttcgttgctttcttgctttcttgctttcttgcttgcttgcttgcttgcttgcttgcttgcttgcttgtcttgcttgc
+spp3 agtgagtgaaaagtgatggatggatggatggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtagagtaggtagg
+spp4 actaactaaaaactaatcaatcaatcaatactaactaactaactaactaactaactaactaactaactaactaactaactaactaactaaactaactaac
+spp5 acagacagaaaacagaacgaacgaacgaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagacaagcaagc
diff --git a/tests/quick_analysis/user_tree/partition_finder.cfg b/tests/quick_analysis/user_tree/partition_finder.cfg
new file mode 100644
index 0000000..e1c7844
--- /dev/null
+++ b/tests/quick_analysis/user_tree/partition_finder.cfg
@@ -0,0 +1,33 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+user_tree_topology = tree.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = all;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
diff --git a/tests/quick_analysis/user_tree/random.phy b/tests/quick_analysis/user_tree/random.phy
new file mode 100644
index 0000000..b4e17fa
--- /dev/null
+++ b/tests/quick_analysis/user_tree/random.phy
@@ -0,0 +1,7 @@
+5 100
+
+spp1 actgactgaaaactgatcgatcgatcgatgctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagactagctagc
+spp2 tctgtctgttttttgttcgttcgttcgttgctttcttgctttcttgctttcttgcttgcttgcttgcttgcttgcttgcttgcttgcttgtcttgcttgc
+spp3 agtgagtgaaaagtgatggatggatggatggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtagagtaggtagg
+spp4 actaactaaaaactaatcaatcaatcaatactaactaactaactaactaactaactaactaactaactaactaactaactaactaactaaactaactaac
+spp5 acagacagaaaacagaacgaacgaacgaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagacaagcaagc
diff --git a/tests/quick_analysis/user_tree/tree.phy b/tests/quick_analysis/user_tree/tree.phy
new file mode 100644
index 0000000..9a12849
--- /dev/null
+++ b/tests/quick_analysis/user_tree/tree.phy
@@ -0,0 +1 @@
+(((spp4,spp1),spp3,spp2),spp5);
diff --git a/tests/quick_analysis/windowslinebreaks/partition_finder.cfg b/tests/quick_analysis/windowslinebreaks/partition_finder.cfg
new file mode 100644
index 0000000..8ad8e9b
--- /dev/null
+++ b/tests/quick_analysis/windowslinebreaks/partition_finder.cfg
@@ -0,0 +1,36 @@
+#NB Don't forget the semi-colons at the end of every statement!
+
+## ALIGNMENT FILE ##
+# the name of your phylip alignment
+alignment = random.phy;
+
+## BRANCHLENGTHS ##
+# 'linked' or 'unlinked'. Most people will want 'linked'
+branchlengths = linked;
+
+## MODELS OF EVOLUTION ##
+# 'all', 'mrbayes', 'raxml', or a comma-separated list of models like this 'GTR+G, GTR+I+G'
+models = GTR;
+
+# model selection: 'AIC', 'AICc', or 'BIC'
+model_selection = BIC;
+
+## PARTITIONS ##
+# e.g. 'part_1 = 1-15\3' or 'part_1 = 1-400 700-1000'
+[data_blocks]
+p1 = 1-20;
+p2 = 21-40;
+p3 = 41-60;
+p4 = 61-80;
+p5 = 81-100;
+
+## SCHEMES ##
+# 'all' (all possible schemes), 'user' (just the scheme below), or 'greedy' (a simple and quick search algorithm)
+[schemes]
+search = user;
+
+#user schemes. Only used if 'search = user'. See manual for how to define.
+s1 = (p1, p2, p3, p4, p5);
+s2 = (p1, p2) (p3, p4, p5);
+s3 = (p1, p2) (p3) (p4, p5);
+s4 = (p1, p5) (p3, p4) (p2);
diff --git a/tests/quick_analysis/windowslinebreaks/random.phy b/tests/quick_analysis/windowslinebreaks/random.phy
new file mode 100644
index 0000000..6cc6299
--- /dev/null
+++ b/tests/quick_analysis/windowslinebreaks/random.phy
@@ -0,0 +1,7 @@
+5 100
+
+spp1 actgactgaaaactgatcgatcgatcgatgctagctagctagctagctagctagctagctagctagctagctagctagctagctagctagactagctagc
+spp2 tctgtctgttttttgttcgttcgttcgttgctttcttgctttcttgctttcttgcttgcttgcttgcttgcttgcttgcttgcttgcttgtcttgcttgc
+spp3 agtgagtgaaaagtgatggatggatggatggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtaggtagagtaggtagg
+spp4 actaactaaaaactaatcaatcaatcaatactaactaactaactaactaactaactaactaactaactaactaactaactaactaactaaactaactaac
+spp5 acagacagaaaacagaacgaacgaacgaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagcaagacaagcaagc
diff --git a/tests/test_alignment.py b/tests/test_alignment.py
new file mode 100644
index 0000000..0c19cf4
--- /dev/null
+++ b/tests/test_alignment.py
@@ -0,0 +1,109 @@
+import pytest
+import fnmatch
+import os
+from StringIO import StringIO
+from partfinder.alignment import Alignment, SubsetAlignment
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+MISC_PATH = os.path.join(HERE, 'misc')
+
+BASIC = """
+5 10
+spp1 actgactgaa
+spp2 tctgtctgtt
+spp3 agtgagtgaa
+spp4 actaactaaa
+spp5 acagacagaa
+"""
+
+INTERLEAVED = """
+5 30
+spp1 actgactgaa
+spp2 tctgtctgtt
+spp3 agtgagtgaa
+spp4 actaactaaa
+spp5 acagacagaa
+
+actgactgaa
+tctgtctgtt
+agtgagtgaa
+actaactaaa
+acagacagaa
+
+actgactgaa
+tctgtctgtt
+agtgagtgaa
+actaactaaa
+acagacagaa
+"""
+
+
+def write_and_get_stream(align):
+ # write out and read back in
+ out = StringIO()
+ align.write_phylip(out)
+ str_output = out.getvalue()
+ del out
+ return str_output
+
+
+def test_simple():
+ a = Alignment()
+ a.parse(BASIC)
+ assert a.species_count == 5
+ assert a.sequence_length == 10
+ assert a.data.shape == (5, 10)
+
+ b = Alignment()
+ b.parse(write_and_get_stream(a))
+
+ assert (a.data == b.data).all()
+ assert a.species == b.species
+
+
+def test_interleaved():
+ a = Alignment()
+ a.parse(INTERLEAVED)
+ assert a.species_count == 5
+ assert a.sequence_length == 30
+ assert a.data.shape == (5, 30)
+
+
+class FakeSubset(object):
+ def __init__(self, cols):
+ self.columns = cols
+
+
+def test_subset():
+ a = Alignment()
+ a.parse(INTERLEAVED)
+
+ ss = FakeSubset([0, 1, 5, 7])
+ b = SubsetAlignment(a, ss)
+ assert b.sequence_length == len(ss.columns)
+ for i, c in enumerate(ss.columns):
+ assert (b.data[:, i] == a.data[:, c]).all()
+
+
+def generate_phyml_paths():
+ paths = []
+ for pth in os.listdir(MISC_PATH):
+ if fnmatch.fnmatch(pth, "*.phy"):
+ paths.append(os.path.join(MISC_PATH, pth))
+
+ return paths
+
+
+ at pytest.fixture(params=generate_phyml_paths())
+def phyml_path(request):
+ return request.param
+
+
+def test_load_and_save_phy(phyml_path):
+ a = Alignment()
+ a.read(phyml_path)
+ b = Alignment()
+ b.parse(write_and_get_stream(a))
+
+ assert (a.data == b.data).all()
+ assert a.species == b.species
diff --git a/tests/test_options.py b/tests/test_options.py
new file mode 100644
index 0000000..f3e6aef
--- /dev/null
+++ b/tests/test_options.py
@@ -0,0 +1,23 @@
+# from partfinder import options, threadpool
+# import shlex
+
+#def pytest_generate_tests(metafunc):
+# # This function feeds the output of the above function into the tests below
+# metafunc.parametrize(
+# 'good_args', [
+# '-p 3 -v folder',
+# 'folder',
+# ]
+# )
+
+# def test_processes():
+# o = options.Options()
+# o.parse_args(shlex.split('folder'))
+# assert o.processes == threadpool.get_cpu_count()
+# assert o.folder_path == 'folder'
+#
+# o = options.Options()
+# o.parse_args(shlex.split('-p 3 folder'))
+# assert o.processes == 3
+#
+
diff --git a/tests/test_parser.py b/tests/test_parser.py
new file mode 100644
index 0000000..f8f9123
--- /dev/null
+++ b/tests/test_parser.py
@@ -0,0 +1,39 @@
+from partfinder.config import Configuration
+from partfinder.parser import Parser
+
+def test_one():
+ # Just use the defaults
+ c = Configuration()
+ c.init()
+ p = Parser(c)
+ p.parse_configuration(test1)
+ assert len(c.user_subsets) == 9
+ assert len(c.user_schemes) == 6
+
+test1 = r"""
+alignment = test.phy;
+branchlengths = linked;
+models = GTR;
+model_selection = BIC;
+
+[data_blocks]
+Gene1_pos1 = 1-789\3;
+Gene1_pos2 = 2-789\3;
+Gene1_pos3 = 3-789\3;
+Gene2_pos1 = 790-1449\3;
+Gene2_pos2 = 791-1449\3;
+Gene2_pos3 = 792-1449\3;
+Gene3_pos1 = 1450-2208\3;
+Gene3_pos2 = 1451-2208\3;
+Gene3_pos3 = 1452-2208\3;
+
+[schemes]
+# search = greedy;
+search = user;
+allsame = (Gene1_pos1, Gene1_pos2, Gene1_pos3, Gene2_pos1, Gene2_pos2, Gene2_pos3, Gene3_pos1, Gene3_pos2, Gene3_pos3);
+by_gene = (Gene1_pos1, Gene1_pos2, Gene1_pos3) (Gene2_pos1, Gene2_pos2, Gene2_pos3) (Gene3_pos1, Gene3_pos2, Gene3_pos3);
+1_2_3 = (Gene1_pos1, Gene2_pos1, Gene3_pos1) (Gene1_pos2, Gene2_pos2, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+1_2_3_by_gene = (Gene1_pos1) (Gene1_pos2) (Gene1_pos3) (Gene2_pos1) (Gene2_pos2) (Gene2_pos3) (Gene3_pos1) (Gene3_pos2) (Gene3_pos3);
+12_3 = (Gene1_pos1, Gene1_pos2, Gene2_pos1, Gene2_pos2, Gene3_pos1, Gene3_pos2) (Gene1_pos3, Gene2_pos3, Gene3_pos3);
+12_3_by_gene = (Gene1_pos1, Gene1_pos2) (Gene1_pos3) (Gene2_pos1, Gene2_pos2) (Gene2_pos3) (Gene3_pos1, Gene3_pos2) (Gene3_pos3);
+"""
diff --git a/tests/test_raxml.py b/tests/test_raxml.py
new file mode 100644
index 0000000..06e96a4
--- /dev/null
+++ b/tests/test_raxml.py
@@ -0,0 +1,46 @@
+import os
+from partfinder import raxml
+from partfinder.config import Configuration
+import numpy
+
+HERE = os.path.abspath(os.path.dirname(__file__))
+MISC_PATH = os.path.join(HERE, 'misc')
+
+def test_parse_nucleotide():
+ pth = os.path.join(MISC_PATH, 'raxml_nucleotide.output')
+ c = Configuration().init(datatype='DNA', phylogeny_program="raxml")
+ p = raxml.Parser(c)
+ res = p.parse(open(pth).read())
+ expected = numpy.array([
+ 0.315909,
+ 0.232955,
+ 0.190909,
+ 0.260227,
+ ])
+ assert numpy.allclose(res.freqs[0], expected)
+
+def test_parse_aminoacid():
+ pth = os.path.join(MISC_PATH, 'raxml_aminoacid.output')
+ c = Configuration().init(datatype='protein', phylogeny_program="raxml")
+ p = raxml.Parser(c)
+ res = p.parse(open(pth).read())
+ expected = numpy.array([0.046704, 0.017460, 0.068093, 0.030991, 0.003492,
+ 0.021388, 0.027499, 0.064164, 0.027499, 0.131820,
+ 0.121781, 0.019642, 0.061545, 0.073330, 0.035356,
+ 0.102139, 0.048014, 0.025753, 0.035356, 0.037975])
+ assert numpy.allclose(res.freqs[0], expected)
+
+def test_parse_lg4m():
+ pth = os.path.join(MISC_PATH, 'raxml_aminoacid_LG4M+G.output')
+ c = Configuration().init(datatype='protein', phylogeny_program="raxml")
+ p = raxml.Parser(c)
+ res = p.parse(open(pth).read())
+
+ # Make sure we got the first block of rates
+ expected = numpy.array([0.082276, 0.055172, 0.043853, 0.053484,
+ 0.018957, 0.028152, 0.046679, 0.15781701,
+ 0.033297, 0.028284, 0.054284, 0.025275,
+ 0.023665, 0.041874, 0.063071, 0.066501,
+ 0.065424, 0.023837, 0.038633, 0.049465])
+ assert numpy.allclose(res.freqs[0], expected)
+
diff --git a/tests/test_submodels.py b/tests/test_submodels.py
new file mode 100644
index 0000000..e9a6cac
--- /dev/null
+++ b/tests/test_submodels.py
@@ -0,0 +1,27 @@
+from partfinder.submodels import get_submodels, count_all_schemes
+
+def test_consistency():
+ known_results = [
+ [0, 0, 0, 0],
+ [0, 0, 0, 1],
+ [0, 0, 1, 0],
+ [0, 0, 1, 1],
+ [0, 0, 1, 2],
+ [0, 1, 0, 0],
+ [0, 1, 0, 1],
+ [0, 1, 0, 2],
+ [0, 1, 1, 0],
+ [0, 1, 1, 1],
+ [0, 1, 1, 2],
+ [0, 1, 2, 0],
+ [0, 1, 2, 1],
+ [0, 1, 2, 2],
+ [0, 1, 2, 3],
+ ]
+ submodels = get_submodels(4)
+ assert submodels == known_results
+
+def test_scheme_lengths():
+ assert count_all_schemes(1) == 1
+ assert count_all_schemes(5) == 52
+ assert count_all_schemes(10) == 115975
diff --git a/tests/test_subset.py b/tests/test_subset.py
new file mode 100644
index 0000000..03a4e4e
--- /dev/null
+++ b/tests/test_subset.py
@@ -0,0 +1,41 @@
+import pytest
+from partfinder.subset import Subset
+from partfinder.scheme import Scheme, SchemeError
+from partfinder.config import Configuration
+
+# TODO: put all of the subset splitting joining tests in here
+
+def test_identity():
+ c = Configuration()
+ c.init()
+
+ s1 = Subset(c, set(range(10)))
+ s2 = Subset(c, set(range(20)))
+ s3 = Subset(c, set(range(10, 20)))
+ s4 = Subset(c, set(range(20)))
+
+ # Not just equal BUT THE SAME (see the __new__ member of the class Subset)
+ assert s1 is not s2
+ assert s1 is not s3
+ assert s2 is s4
+
+
+def test_overlap(caplog):
+ c = Configuration()
+ c.init()
+
+ s1 = Subset(c, set(range(10)))
+ s2 = Subset(c, set(range(10, 20)))
+ s3 = Subset(c, set(range(9, 20)))
+
+ # This should be okay...
+ Scheme(c, 'a', [s1, s2])
+
+ # This isn't
+ with pytest.raises(SchemeError):
+ Scheme(c, 'a', [s1, s3])
+ assert "contains overlapping" in caplog.text()
+
+
+
+
diff --git a/tests/test_tiger.py b/tests/test_tiger.py
new file mode 100644
index 0000000..e539c7f
--- /dev/null
+++ b/tests/test_tiger.py
@@ -0,0 +1,97 @@
+from partfinder._tiger import TigerDNA
+from partfinder.alignment import Alignment
+import numpy as np
+import pytest
+
+test_alignments = {
+"small1" : """
+5 10
+spp1 actgactgaa
+spp2 tctgtctgtt
+spp3 agtgagtgaa
+spp4 actaactaaa
+spp5 acagacagaa
+""",
+"small2" : """
+4 11
+s1 GTGCTGGTGCT
+s2 AGCCTGGTGCT
+s3 AAGCTGGTGCT
+s4 CGTCTGGTGCT
+""",
+"large1" : """
+4 500
+s1 CTTGAGGTTCAGAATGGTAATGAAGTGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCCATGGGTTCTTCCGACGGTCTGCGTCGCGGTCTGGATGTAAAAGACCTCGAGCACCCGATCGAAGTCCCAGTTGGTAAAGCAACACTGGGTCGTATCATGAACGTACTGGGTCAGCCAGTAGACATGAAGGGCGACATCGGTGAAGAAGAGCGTTGGGCTATCCACCGTGAAGCACCATCCTATGAAGAGCTGTCAAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTTGCGAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTTATTCGTAACATCGCGATCGAGCACTCCGGTTATTCTGTGTTTGCGGGCGTAGGTGAACGTACTCGTGAGGGTAACGACTTCTACCAC [...]
+s2 CTTGAGGTACAAAATGGTAATGAGAGCCTGGTGCTGGAAGTTCAGCAGCAGCTCGGTGGTGGTATCGTACGTGCTATCGCCATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTTAAAGACCTTGAGCACCCGATCGAAGTCCCGGTTGGTAAAGCAACGCTGGGTCGTATCATGAACGTGCTGGGTCAGCCGATCGATATGAAAGGCGACATCGGCGAAGAAGAACGTTGGGCGATTCACCGTGCAGCACCTTCCTATGAAGAGCTCTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATGTGTCCGTTCGCGAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTTGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAACACTCCGGTTACTCCGTGTTTGCTGGTGTTGGTGAGCGTACTCGTGAGGGTAACGACTTCTACCAC [...]
+s3 CTTGAGGTACAGAATAACAGCGAGAAGCTGGTGCTGGAAGTTCAGCAGCAGCTCGGCGGCGGTATCGTACGTACCATCGCAATGGGTTCTTCCGACGGTCTGCGTCGTGGTCTGGAAGTGAAAGACCTCGAGCACCCGATCGAAGTCCCGGTAGGTAAAGCGACCCTGGGTCGTATCATGAACGTGCTGGGTCAGCCAATCGATATGAAAGGCGACATCGGCGAAGAAGATCGTTGGGCGATTCACCGCGCAGCACCTTCCTATGAAGAGCTGTCCAGCTCTCAGGAACTGCTGGAAACCGGCATCAAAGTTATCGACCTGATTTGTCCGTTCGCTAAGGGCGGTAAAGTTGGTCTGTTCGGTGGTGCGGGCGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGATCGAGCACTCCGGTTACTCCGTGTTTGCAGGCGTGGGTGAGCGTACTCGTGAGGGTAACGACTTCTACCAC [...]
+s4 CTCGAGGTGAAAAATGGTGATGCTCGTCTGGTGCTGGAAGTTCAGCAGCAGCTGGGTGGTGGCGTGGTTCGTACCATCGCCATGGGTACTTCTGACGGCCTGAAGCGCGGTCTGGAAGTTACCGACCTGAAAAAACCTATCCAGGTTCCGGTTGGTAAAGCAACCCTCGGCCGTATCATGAACGTATTGGGTGAGCCAATCGACATGAAAGGCGACCTGCAGAATGACGACGGCACTGTAATTCACCGTGCAGCACCTTCGTATGAAGATCAGTCTAACTCGCAGGAACTGCTGGAAACCGGCATCAAGGTTATCGACCTGATGTGTCCGTTCGCTAAGGGCGGTAAAGTCGGTCTGTTCGGTGGTGCGGGTGTAGGTAAAACCGTAAACATGATGGAGCTGATCCGTAACATCGCGGCTGAGCACTCAGGTTATTCGGTATTTGCTGGTGTGGGTGAGCGTACTCGTGAGGGTAACGACTTCTACCAC [...]
+"""
+}
+
+ at pytest.fixture(scope="module", params=test_alignments.keys())
+def alignment_text(request):
+ return test_alignments[request.param]
+
+def test_tigger(alignment_text):
+ a = Alignment()
+ a.parse(alignment_text)
+ bitsets, slow_rates = slow_tiger(a)
+ tigger = TigerDNA()
+ tigger.build_bitsets(a)
+ fast_rates = tigger.calc_rates()
+ assert np.allclose(slow_rates, fast_rates)
+
+
+def slow_tiger(alm):
+ denom = float(alm.sequence_length - 1)
+ # Initiate a list to store the bitsets for each set partition
+ set_parts = []
+ # Loop through the sites in each aligment to generate bitsets
+ for site in alm.data.T:
+ sites = []
+ # Generate a bitset for each nucleotide. First see if there are any N's,
+ # if there are, you must create bitsets for each nucleotide. Note: Make
+ # sure that all ambiguous characters have been converted to N's prior to
+ # running, i.e. all '-' should be 'N'
+ N = (site == ord('N'))
+ for nuc in map(ord, list('ACGT')):
+ # Add the bitset ONLY if it is non-empty
+ sb = (site == nuc)
+ if np.any(sb) or np.any(N):
+ sites.append(sb)
+ if np.any(N):
+ for s in sites:
+ s |= N
+ set_parts.append(sites)
+
+ # Initiate a list to store the rates
+ rates = []
+ # Look at each set partition in the alignment
+ for i, sp_i in enumerate(set_parts):
+ rate = 0.0
+ # Now compare it against every other set partition in the alignment,
+ # except for itself
+ for j, sp_j in enumerate(set_parts):
+ # Do not compare the site against itself
+ if j == i:
+ continue
+
+ # Keep track of the number of comparisons done
+ num = 0.0
+ # 'axpi' refers to the compatibility of one bitset to another. If
+ # the bitset is a subset of another, the axpi is 1, otherwise it
+ # is 0
+ axpi = 0.0
+ # Check each partition set from site pattern j to see if it is a
+ # site pattern i
+ for ps in sp_j:
+ for ps2 in sp_i:
+ if np.array_equal((ps & ps2), ps):
+ axpi += 1.0
+ break
+ num += 1.0
+ rate += axpi / num
+
+ rate /= denom
+ rates.append(rate)
+ return set_parts, rates
diff --git a/timings/array_lookups.py b/timings/array_lookups.py
new file mode 100644
index 0000000..4050c20
--- /dev/null
+++ b/timings/array_lookups.py
@@ -0,0 +1,179 @@
+# array lookups
+
+import numpy as np
+import random
+import sklearn.metrics.pairwise
+import scipy.spatial.distance
+import heapq
+from bisect import insort
+from itertools import islice
+from scipy.spatial import KDTree
+
+
+
+N = 1000
+r = np.array([random.randrange(1, 1000) for _ in range(0, 10000)])
+c = r[:, None]
+
+dists = scipy.spatial.distance.pdist(c, 'cityblock')
+
+def method1(dists, N):
+ d_sq = scipy.spatial.distance.squareform(dists)
+ unique_dists = np.unique(dists)[:N]
+ l = []
+ for d in unique_dists:
+ locations = np.where(d_sq==d)
+
+ for i in range(len(locations[0])):
+ pair = [locations[0][i], locations[1][i]]
+ l.append(pair)
+ return l
+
+
+
+def condensed_to_square_index(n, c):
+ # converts an index in a condensed array to the
+ # pair of observations it represents
+ # modified from here: http://stackoverflow.com/questions/5323818/condensed-matrix-function-to-find-pairs
+ ti = np.triu_indices(n, 1)
+ return ti[0][c]+ 1, ti[1][c]+ 1
+
+def condensed_to_square_index2(ti, c):
+ return ti[0][c]+ 1, ti[1][c]+ 1
+
+
+def method2(dists, N):
+ closest = dists.argsort()[:N]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ r = []
+ for i in closest:
+ pair = condensed_to_square_index(n, i)
+ r.append(pair)
+ return r
+
+
+def method3(dists, N):
+ closest = dists.argsort()[:N]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = np.vstack(ti)[:, closest] + 1
+ return r
+
+def method4(dists, N):
+ closest = dists.argsort()[:N]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = zip(ti[0][closest] + 1, ti[1][closest] + 1)
+ return r
+
+def method5(dists, N):
+ closest = dists.argsort()[:N]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = np.column_stack((np.take(ti[0], closest), np.take(ti[1], closest))) + 1
+ return r
+
+
+def method6(dists, N):
+ closest = dists.argsort()[:N]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = []
+ for i in closest:
+ pair = condensed_to_square_index2(ti, i)
+ r.append(pair)
+ return r
+
+def argsmallest_n(a, n):
+ ret = np.argpartition(a, n)[:n]
+ b = np.take(a, ret)
+ return np.take(ret, np.argsort(b))
+
+# NB method7 requires NumPy 1.8
+def method7(dists, N):
+ closest = argsmallest_n(dists, N)
+ n = np.ceil(np.sqrt(2* len(dists)))
+ tu = np.triu_indices(n, 1)
+ pairs = np.column_stack((np.take(tu[0], closest), np.take(tu[1], closest))) + 1
+ return pairs
+
+def method8(dists, N):
+ closest = heapq.nsmallest(N, dists)
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = zip(ti[0][closest] + 1, ti[1][closest] + 1)
+ return r
+
+
+def method9(dists, N, insort=insort):
+ # http://stackoverflow.com/questions/350519/getting-the-lesser-n-elements-of-a-list-in-python
+ it = iter(dists)
+ closest = sorted(islice(it, N))
+ for el in it:
+ if el <= closest[-1]: #NOTE: equal sign is to preserve duplicates
+ insort(closest, el)
+ closest.pop()
+
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = zip(ti[0][closest] + 1, ti[1][closest] + 1)
+ return r
+
+def method10(dists, N):
+ # http://stackoverflow.com/questions/350519/getting-the-lesser-n-elements-of-a-list-in-python
+ mins = dists[:N]
+ mins.sort()
+ for i in dists[N:]:
+ if i <= mins[-1]:
+ np.append(mins, i)
+ mins.sort()
+ mins = mins[:N]
+ closest = [np.where(dists==x) for x in mins]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = zip(ti[0][closest] + 1, ti[1][closest] + 1)
+ return r
+
+
+def method11(dists, N):
+ # http://stackoverflow.com/questions/350519/getting-the-lesser-n-elements-of-a-list-in-python
+ mins = list(dists[:N])
+ mins.sort()
+ for i in dists[N:]:
+ if i <= mins[-1]:
+ mins.append(i)
+ insort(mins, i)
+ mins = mins[:N]
+
+ closest = [np.where(dists==x) for x in mins]
+ n = np.ceil(np.sqrt(2* len(dists)))
+ ti = np.triu_indices(n, 1)
+ r = zip(ti[0][closest] + 1, ti[1][closest] + 1)
+ return r
+
+
+def method12(dists, N):
+ tree = KDTree(dists, leafsize=dists.shape[0]+1)
+ distances, ndx = tree.query(0, k=N)
+
+def method4_2(dists, N):
+ closest = dists.argsort()[:N]
+
+# timing in ipython, best is method 4 when the array is 1000 by 1000, and N = 1000
+
+# best method is 9 when array gets > ~6000 by 6000, and 9 is only marginally slower for smaller arrays
+
+# but note that either using the bottleneck module, or method7 (both of which use
+# efficient sorting) would be a lot quicker.
+
+
+# NB arrays of 10k by 10k still take ~20s with method 4. This is not great.
+
+
+
+
+
+
+
+
+
diff --git a/timings/numpy_vs_set.py b/timings/numpy_vs_set.py
new file mode 100644
index 0000000..656f6b4
--- /dev/null
+++ b/timings/numpy_vs_set.py
@@ -0,0 +1,42 @@
+import timeit
+setup_fmt = """
+import random
+from hashlib import md5
+from cPickle import dumps
+from numpy import union1d, concatenate, array
+
+cols = range({0})
+x = random.sample(cols, {1})
+y = random.sample(cols, {1})
+x1 = set(x)
+y1 = set(y)
+x2 = array(x)
+y2 = array(y)
+
+def meth0():
+ q = x1 | y1
+ c = list(q)
+ c.sort()
+ x = md5(dumps(c, -1)).hexdigest()
+ return q, c, x
+
+def meth1():
+ q = union1d(x2, y2)
+ # q = concatenate((x2, y2))
+ # q.sort()
+ x = md5(q.tostring()).hexdigest()
+ return q, x
+"""
+
+if __name__ == '__main__':
+ rep = 3
+ number = 100
+ for column_size in 100, 1000, 10000, 100000:
+ print 'using array size\t{0} ----'.format(column_size)
+ sample_size = column_size/10
+ setup = setup_fmt.format(column_size, sample_size)
+ t_set = min(timeit.repeat('meth0()', setup=setup, repeat=rep, number=number))
+ t_numpy = min(timeit.repeat('meth1()', setup=setup, repeat=rep, number=number))
+ print "using sets\t{:.6f}\nusing numpy\t{:.6f}".format(t_set, t_numpy)
+
+
--
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