[med-svn] [phyml] 01/01: Autopkgtest fixed

Canberk Koç cbk-guest at moszumanska.debian.org
Wed Oct 12 20:57:34 UTC 2016 

This is an automated email from the git hooks/post-receive script.

cbk-guest pushed a commit to branch master
in repository phyml.

commit 4908224456491b258e1658a99738a494fdb4bd34
Author: Canberk Koç <canberkkoc at gmail.com>
Date:   Wed Oct 12 23:56:53 2016 +0300

    Autopkgtest fixed
---
 debian/changelog                  |   6 +-
 debian/phyml-examples/example.nex | 472 ++++++++++++++++++++++++++++++++++++++
 debian/phyml.examples             |   1 +
 debian/tests/run-unit-test        |   2 +-
 4 files changed, 478 insertions(+), 3 deletions(-)

diff --git a/debian/changelog b/debian/changelog
index d3487d7..a99ee86 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -4,7 +4,7 @@ phyml (3:3.2.0+dfsg-3) UNRELEASED; urgency=medium
 
   [ Canberk Koç ]
   * autopkgtest added
-
+  * fix autopkgtest 
   [ Andreas Tille ]
   * Add missing Depends: openmpi-bin
   * use wrapper to select MPI version if applicable
@@ -12,7 +12,9 @@ phyml (3:3.2.0+dfsg-3) UNRELEASED; urgency=medium
   * Fix missing declaration
   * hardening=+all,-pie
 
- -- Canberk Koç <canberkkoc at gmail.com>  Wed, 20 Jul 2016 03:01:14 +0300
+ 
+
+ -- Canberk Koç	 <canberkkoc at gmail.com>  Wed, 12 Oct 2016 23:51:39 +0300
 
 phyml (3:3.2.0+dfsg-2) unstable; urgency=medium
 
diff --git a/debian/phyml-examples/example.nex b/debian/phyml-examples/example.nex
new file mode 100644
index 0000000..38f367b
--- /dev/null
+++ b/debian/phyml-examples/example.nex
@@ -0,0 +1,472 @@
+#NEXUS
+BEGIN DATA;
+DIMENSIONS NTAX=7 NCHAR=2888;
+FORMAT DATATYPE=DNA;
+
+MATRIX
+
+ENSG00000048405     --------------------------------------------------
+ENSMUSG00000039841  --------------------------------------------------
+ENSDARG00000004594  GTCCTTAATTTCCTTAGTTTGATGCACACGTTGTGGGGGTCAGATGTAAA
+ENSDARG00000039843  --------------------------------------------------
+ENSGACG00000018833  --------------------------------------------------
+ENSORLG00000013219  --------------------------------------------------
+ENSTNIG00000018490  --------------------------------------------------
+
+--------------------------------------------------
+--------------------------------------------------
+TCACCAATCTGGCGACAACATCGGGTGCCACATTTTGGTGGTCTCAAACA
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+
+--------------------------------------------------
+--------------------------------------------------
+TCCATTGCACCTTTGCGCAACAGCCGCTTCTCCGCCGAGAGGTCCTCGCG
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+
+--------------------------------------------------
+--------------------------------------------------
+GTGCACAAAGGCAGCTTCCGAGAGGGCAGCGTCAGCGCGGAGGCGAGAGA
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+
+--------------------------------------------------
+--------------------------------------------------
+AACAATCTCCAGATCGCCTTCTACCATCTTTACTCGAAAGCGAACGTTGT
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+
+-----------------------AT-------GCC---TTTAAGG-----
+-----------------------AT-------GCC---TTTGAGG-----
+TTTTACACGAGCCTTTTAGGTTCATAAAAGGGGCC---TCTGAGATGGAG
+-----------------------ATGGAGGAAGCTCCGTCCAATG-----
+--------------------------------------------------
+--------------------------------------------------
+--------------------------------------------------
+
+------------------------------------GACAAATACTGTCA
+------------------------------------GACAAATACTGTCA
+GCTACTAAGAGTGAAGTTCAGGGAAGCCTGACTAGTGACAAATACTGCCA
+-------------------------------------AAAAATCTTGCCA
+---------------------------------AAAAATGAATATTGCAA
+--------------------------------------------------
+--------------------------------------------------
+
+GACTGA------------CCACCATCATCA-----CGGA-----------
+AACGGA------------CCACCATCATCA-----CGGA-----------
+GACTGAGACACTTCAGGCCTGCTGTTGCCAAACAACAGAAACCCCTCAAG
+GACGGA-------------TGTCTCTCCTGGAT--CTGA-----------
+ATCATA------------TCGCAAATGCAG--------------------
+--------------------------------------------------
+--------------------------------------------------
+
+-----TGCTGTGAA----CCAGTTTATATCCTGGAACCTGGAGATCCTCC
+-----TGCTGCGAA----CCAGTTTATATCCTGGAGCCTGGAGATCCTCC
+AGCCTTGTGGCAAAAAT-CCAGTGCATCTGATTGAGCCTGGTGATCCACC
+--TCATCCCATCAAGACACCAGTTTACTCAACAGAACCAGGAGATCCTCC
+-------CAGTGAA-------AGTTTCTGTGTGGAGCCTGGAGATCCTCC
+---------------------------------GAGCCTGGTGATCCTCC
+------------------------------GTGGAACCTGGAGACCCTCC
+
+TTTGTTACAGCAACCACTACAGACATCCAAATCTGGTATTCAACAAATAA
+CTTGTTACAGCAACCAGTGCAGACATCCAAATCTGGTATTCAGCAAATAA
+CCTGCTTCAACAACAGCTTCAGACATCCAAGTCAGGAATTCATCAAATTA
+CTTACTCCAAACCCCAATGCTCACCTCTAAATCTGGCATCCAGCAGATCA
+CCTGCTCCAGCAGCCTCTGCAGACCTCCAAATCCGGGATCCAGCAGATAA
+TCTTCTTCAGCAGCCTCTGCAGACCTCCAAGTCAGGGATTCAGCAGATCA
+CCTGCTTCAGCAGCCTCTGCAGACCTCCAAATCTGGGATCCAGCAGATCA
+
+TTGAGTGCTTTCGATCAGGAACTAAACAACTTAAGCATATTTTATTAAAA
+TTGAGTGCTTTCGATCAGGAACCAAACAACTTAAACATATTTTATTAAAA
+TTGAGTGTTTTCGCTCAGGTACAGCTCAACTAAAACAAATGCTGTTGAAG
+TTGAGTGTTTCCGCACAGGTACTGCACAGCTGAAGCACATTCTCCTGAAA
+TCGAATGCTTCCGCTCAGGCACCAGCCAGCTGAAACACATGCTGCTGAGG
+TTGAATGCTTCAGATCAGGCACCAGCCAGCTGAAGCACATCCTGTTACAG
+TCGAGTGCTTCCGCTCAGGAACAGCTCAGCTCAAACACATGCTGCTGAGG
+
+GATGTGGACACTATTTTTGAATGTAAGTTATGCCGCAGTCTCTTCAGAGG
+GATGTGGACACTATTTTTGAATGTAAATTATGCCGTAGTCTCTTTAGAGG
+GAAGTTGACACCATATTTGAATGTAAAATCTGTCGAAGTCTGTTTCGTGG
+GAGGTGGACACCATCTTTGAATGTAAACTCTGCCGCAGTCTCTTCCGTGG
+GAGGTGGACACCATCTTTGAGTGCAAACTGTGTCGCAGTCTGTTCAGAGG
+GAGGTGGACACCATCTTTGAGTGTAAAATTTGCCGCAGCCTTTTCAGGGG
+GAGGTGGACACCATCTTTGAATGTAAGCTGTGCAGGAGTCTGTTCAGAGG
+
+ATTACCAAATTTAATTACCCATAAAAAATTCTACTGC-----CCAC-CAA
+ATTACCAAATTTAATTACCCATAAAAAATTTTACTGC-----CCAC-CAA
+TCTACCAAATCTGGTCACACACAAGGAGCTTTACTGCTTTTCCCAG-CAA
+CCTTCCTAATCTGATCAAACACAGAGAAATGTACTGTT----TCACTCGA
+CCTGCCCAACCTCATCACGCACAGAGAGTACTACTGCC----TACCCCGG
+CCTGCCCAACCTCATCACGCACAAGGAGTACTACTGCT----TATCCCGC
+CCTGCCCAACCTCATCACACACAAGGAGTACTACTGCC----TGACCCGG
+
+GTCTCCAGATGGATGACAACCT------TCCTGATGTAAATGATAAACAA
+GTCTCCAAATGGATGACAATCT------TCCTGATGTAAATGATAAACAA
+--CCTCAGTCAGATGA-----T------CCCT----CAAAAGGTGGGCAG
+ATGCCTGAAC--ATGATGTTCT------TTCTG---TTGATGGCAAGAAG
+CTGCCCGAAC--CCGACG------------------GAGACGACAGACAT
+ATGCCTGAGC--ACGACGATACAAACAGTTCGTCGGGCGATGACAGACAC
+CTGCCTGAAT--ACGACG---------GTTCAGCGGGGGACGACAGGCAG
+
+AGCCAAGCCATAAATGATCTCCTAGAAGCCATATATCCA-AGTGTGGACA
+AGCCAAGCCATAAGTGATCTCCTAGAAGCCATATATCCA-AGAGTGGACA
+AGCCATGCCATCAAAGAACTTCTTCAAGCCATCTATCCACAGAAAGAGCA
+AG------CGTGAAAGAACTTCTTGAAGCCATCTACCCTTACT-CCAATA
+AGTGTGGTCATGAAGGAGTTATCGGAGGT---ATATCCC-AGAGTC----
+AGTGTGGCCATAAAAGACGCACTGGACGCTAAATATTCC-AGAGCGGAGC
+AGCGTAGCCATGAAGGATTTACTGGACGCCATATATCCC-AGATCTGACA
+
+AACGAGAATATATTATTAA-GCTAGAACCCATAGAAACTAATCAAAATGC
+AGAGAGAATATATTATTAA-GCTAGAACCCATAGAAACCAACCAAAATGC
+AG-AAAAACAAACAATTCA-GCTTGAGGCCATTGAGACCAACCCCAATGC
+AAGAGGAATGTGT-ATTAACACTGGAGCCCATTGCCGGCAACCAGAATGC
+--CCGGACTACGTGGTCCG-ACTGGAGCCCATTCGGACCACCAACAAGGC
+GGTCGGACTGTGTTGTCCG-GCTCGAGCCCATTCAGAGCACCACCAAGGC
+AAGCAGATTACGTCGTCCG-ACTGGAGCCGATTCAAACCAGCACTAAGGC
+
+AGTATTTCAATATAT-TTCG---AGGACTGAT---AATCCTATTGAAGTC
+AGTGTTTCAATATAT-TTCA---AGGACTGAT---AACCCTGCTGAAGTG
+AGTGTTCCAACATGT-TTCACT-AGGGGAAATTCAAGACATGCCAGAATC
+TGTGTATCAATACCTGTCCA---AAGACCA--------CAGCCTGGCATC
+CGTGTTCCAGTACCTCGCCACGGAGGAGGAGCT--GGCCAGGATCCCGTC
+CGTGTATCAGTACCTCACCACAGAGGAGGAGCT--GGCCAGATATCCATC
+TGTGTTCCAGTACATCAGCACAGAGGAGGAGCT--GGCCAGATATCCATC
+
+ACA-GAGTCAAGCAGTACT---CCTGAACAAA---CCGAAGTTCAGATA-
+ACC-GAGTCAAGCAGTACA---CCTGAACAAA---CTGAAGTTCAAATA-
+CCCTGCCCCTACTACTACTGCCCCTGCCCCTGTCCCTGAGATTTTATTA-
+T------TCAAGC---------CCTAATCATA--------GCACAAACA-
+GCAGACGCCAAGG--------TCGGTGGCGTGCCAATTTGGTTTTGTCG-
+ACACACAACCAG----------CGCCAGAGAG-------AGTCCAGTAG-
+ACACACACCCAGAGAAAGT--CCGGTGACATGTGAAGGAGAAACCGTTGA
+
+--C---AGGAAACTAG----CACTGA---------ACAGTCAAAAACAGT
+--C---AGGAGACAAG----CTCAGA---------ACAGCTGAAAGCAGT
+--CCTGAGAAGAAAAATCGTCGCAAATCTATTTTGGCACCCAAAAA-GGT
+--GCTGGGGACACAAC--ATCTCAGA----------CAACCAAGAGCTGT
+--TTCAGAGGGAC--------GCGAA-----------AACACGAAGCTCT
+--TGTGGGAGGGT--------GAGGC-----------AACAGAAGGCGCC
+GGCGCCGGAAGACAAT---CAGCCAA-----------ATCAGCAGGCCGC
+
+AC--CGGTTACA----GATACAGAGGTGGAAA------CTGTAGAGCCCC
+CC--CCGACGCA----GATACAGAGGTGGAGGA---GGCCATAGAGCCTC
+CCAACAGTCAGATTTTGAAGATGAGATGGAAACTGAAGTCGAAGAACAAC
+AT-------ACA-------------ATGGAGA-----------------T
+A--------GCA----------GTGTTGAG-----------CGTGACATT
+G--------ACA----------GCAAT--------------CCCACCAAC
+A--------GCA----------GAGAGCAGAGA----GAGCCACGGCAGC
+
+CTCCTGTTG-------AGATT----GTTACAGAT--GA---AGTTGCACC
+CTTCTATAG-------AGACT----GTTGTAGAT--GA---AGCTGCAGC
+CTGCTAATG-------AAGGTCCGAGCTGC-GAT--GAG-CAAATGAAGA
+CCCCTTGGG-------AGAG-----------GAA--GA---AAACGGTTA
+TTTCCCCCGGGGCAGAAGAG-----GTGGGAGGC-CGA---GGAGGAGGC
+CCGCAAGGGGGACAAGAGAGT----GTCGGTAGTGCGAC--GGAGGAGGA
+CC-CGGACAGTATCGAGGAG-----GGCGGAGATGGGAGGCGGAGGAGGA
+
+TACA------TCTGATGAACAACCTCA----GGAGTCGCAGGCTGACTTG
+TCCC------ACTGAGGAGCAACCTCA----GGAATCACAGGCTGACTTG
+TTGA------A--GGGGAGGAAGAGGA----AGAGGAGAGTGCAGCCTCA
+TATA------CACGATGA--------A----AGAG-AGAACGTTGACATA
+GGCAGCGGCGAAGGAGGAGCCGCCGAAGCCCGAGGACGAGGGCTCCACTA
+GGCC------AAAGAGGAGCAGCAGCAACCAGAGGACGAAGGCTCCAACA
+GTCC------AAAGCGGAGCCGACGCAGCACGAAGACGAGGGCTCCACCA
+
+GAAACTTC------------------------------------------
+GAGACGTC------------------------------------------
+GAAG----------------------------------------------
+ATAG----------------------------------------------
+GCGGGGT-------------------------------------------
+GTGGAGT-------------------------------------------
+GCGGGGTAGGCCACCCGAGACTCCGCCAGCACGTTGGACCAAACGCCCTG
+
+-------------------------TGACAATTCTGATTTTGGTCACCAG
+-------------------------TGACAGTTCTGACCTTGGTCACCAG
+-------------------------TAAAAGAATTGAG---GATCTCT--
+---------------------------AGAGAGTAGA-------------
+--------------------------TGAGGACGTGAC---CATATCC--
+--------------------------GGAAGATGTGAC---CATCTCC--
+CTCACGTCACTTCTTTCGATCGAGGTGGAGGACGTGAC---GATCTCC--
+
+TTGATATGTTGTCTTTGTAGAAAAGAATTCAATTCTAGACGAGGTGTTCG
+TTGATATGTTGTCTTTGTAGAAAAGAATTCAATTCTAGACGAGGTGTTCG
+------TGTTGCCTGTGCGGAAAAGACTTTGGCTCTAGACGTAGTGTGCG
+---------------TGCAGACGAAA------------GCAAGGTG----
+------TGCTGTCTGTGCGGTCAGGAATTCAACTCGCGCCGCAGCATCAG
+------TGTTGTCTCTGCGGTCAAGACTTCAACTCGCGCCGCAGCATCAG
+------TGCTGCCTGTGCGGTCAGGACTTCAACTCGAGGCGCAGCATCCG
+
+CCGTCACATTCGAAAAGTACACAAGAAAAAGATGGAAGAACTAAAAAAGT
+TCGTCACATTCGAAAAGTACACAAAAAAAAGATGGAAGAACTAAAAAAAT
+CCGACACTGCCGAAAGATGCATTGGCAGAGGATGGAGGAGCTGCGCAAGT
+-CATCAGGATAGTGAAGAACCCGAGGAGACAACAGAAGAA----GCAGGT
+ACGCCACTGTCGTAAAGTGCACCAGAACAAGCTGGAAGAGCTGCGGAAGT
+GCGCCACTGCCGCAAAATGCACCAGACAAAGCTGGAGGAGCTCAGGAAGT
+ACGCCACTGCCGCAAAATGCACCAGACCAAACTGGAGGAGCTCCGCAAGT
+
+ACATTGAAACACGAA-AGAATCCAAACCAATCCTCTA---------AAGG
+ACATTGAAACACGGA-AGACTCCAAACCAGTCTTCAA---------AAGG
+TTACAGAGACACGCACAGTGCCC--ATCAGTCTCCTGTCAGTGGTTAAGG
+GATCTGGCTTACAAA-TGCATCC-------TCTGCAAC---------AGG
+TCACGGAGACGCGTACGGTTCCG--ACCAGCCTGCTGTCTATGG---GAG
+TCACCGAGACGCGGACGGTTCCT--ACCAGTCTGCTTTCCATGGTGAAAG
+TCACAGAGACGCGCACGGTTCCC--ACGAGCCTGCTGTCCATGGTGAAAG
+
+AC--GCA----GTAAGAATGTTCTAGTTCCATTAAGTAGGAGTTGTCCAG
+AC--GCA----GTAAGAGTGTTCTAGTTTCATTAAGTAGGAGCTGTCCAG
+ACAAGCATCCTGTTGAACCACCGCCGTCTCCT--GGGAAGAGCTGCCCAG
+ACTTACA--------GAGT-TCGAGGCCACCTTAAAAGACACATGCAGAC
+GTCGCCCG-----AGGACACTCAGCACGCCCGCAGGAAAATCCTGCCCGG
+GTCGACAG-----AGAACCCTCAGCACACCGACCGGAAAGTCCTGCCCCG
+GTCGGCCG-----CGGACGCTCAGCACGCCGACCGGAAAATCCTGCCCAG
+
+TATGTTGTAAATCATTTGCTACAAAAGCGAATGTAAGGAGGCATTTTGAT
+TTTGTTGTAAATCATTTGCTACAAAAGCGAATGTAAGGAGGCATTTTGAT
+TGTGCAAAAAGTCATTTGCCACCAAGGCCAATGTTCGTCGTCACTTTGAT
+TGTTCATAAGGTTGTGTCCT-------CTAGTTTGACAAGCAAATCTAAG
+TGTGTTTCAAAAGCTTCGCCACTAAAGCCAACGTGCGTCGCCATTTTGAC
+TGTGCCTCAAGAGCTTTGCAACCAAAGCCAACACCCGGCGCCACTTTGAC
+TGTGCCTCAAATCCTTCGCCACCAAAGCCAACGTGCGCCGCCACTTTGAC
+
+GAAGTTCATAGAGGACTAAGGAGGGATTCAATTACTCCTGATATAGCAAC
+GAAGTTCACAGAGGACTAAGGAGGGATTCAATTACTCCTGATATAGCGAC
+GAGGTCCACCGTGGCTTAAAGCGGGATTTGATTACTCCAGACATTGCCAC
+AAGAT--------GACCAATGGCAAACTTG-------CAGACA--ATCCC
+GAGGTGCACCGCGGCCTACGGAGGGACGCCATCACACCCAGCATCGCTTC
+GAGGTGCATCGAGGTCTGCGGCGGGATTCTATCACGCCCGCCGTCGCCCT
+GAGGTGCATCGCGGCCTGCGGAGGGACACCATCACGCCCAGCATCGCCTC
+
+AAAGCCTGGGCAACCTTTGTTCCTGGATTCTATTTCTCCT--------AA
+AAAGCCTGGGCAGCCTTTGTTCCTGGATTCTGCTTCTCCT--------AA
+AAGACCAGGCCAGCCTCTTTTACTTGACACTCCTTCTCCTCCATCTCCAG
+AATGCAAGCCCAAGCTCTTCATCTGACTCCCAGAGCTC------------
+GCGCCCCGGCCAGCCTTTCTCTCTGGAGGTCACGCCCCCCCG-----GAA
+GAAGCCCGGTCAGCCCTTCCCCCTGGAAACCACGCCTCCGAG-----GAA
+GCAGCCTGGCCCGCCCTTTTCTCCGGAGGCCACACCCCCCAG-----CCA
+
+AAAATCTTTTAAGA----CTCGAAAACAAAAGTCTTCTTCAAAGGCTGAA
+AAAATCTTTTAAGA----CTCGCAAACAAAAGTCT---TCAAAGGCTGAA
+CAAAAGTACCAAGCTCTCCTTTGAAGCAAGA---------AAAACCACAG
+GAAGAATCCCAAGG--------AGAACAAGGATCC------AAAATTCAC
+GAGCAACGCCTCCT----CTCCAACGCGCAGCGGCAGCTCCAAGTCCACG
+GAGCAATAACTCGT----CGCCGACGCGGAGC--CA----CAAGTCCACT
+AAACCAGGCCAAAG----GTCCGA-GCCAGGTG-----TTTGCGGCTTCG
+
+T--ACAA--TTTAACT-----GCATGCAAATGCCTCCTTTGCAAGAGGAA
+T--ACAA--TTTAACT-----GCATGCAAATGCCTCCTTTGCAAGAGGAA
+T--ACAA--CCTGACA-----AGTTGCCGCTGCAAGCTCTGCAAACGCAA
+T--ATAGGTTTTGACTTCAAGACGTGCTTCTGCAAGCTCTGCAGACGGAC
+CCGGCGGCCCCGCCCT------CCAGCCGCTGCGCGCTCTGCAAGAGGAC
+CCCGCCGGGACGACCT------CCTGTCGCTGCACGGTTTGCAAGAGGAA
+CAGGCGAGCCCTGCCT------CATGCCGCTGCACGCTCTGCAAGAGGAA
+
+ATATAGTTCACAAATA------ATGCTTAAAAGACATATGCAAATTGTCC
+ATACAGTTCACAAATA------ATGCTTAAGAGACATATGCAAATTGTCC
+GTACAGCTCCCAACTA------ATGCTTAGGCGACATATGCGAATTGTTC
+ATTCAGCTCCGAGCAG------AACCTGGAGAAGCACAT-TGAGCTGCAC
+CTACAGCTCTCAGCT------CATGTTGAAGAGGCACATGCGCATCGTCC
+CTACAGCTCTCAGCT------CATGTTGAAAAGACACATCCGTATAGTTC
+CTACAGCTCCCAGCTAATCTCCATGTTGAAGAGACACATGCGGATTGTTC
+
+ACAAGATAACTCTTTCTGGAACA-AACTCT--------------------
+ACAAGATAACTCTTTCTGGAGCA-AACTCT--------------------
+ATAAGATA-CCCACTCTAGAAAACAGCTCTCAGAAGTCCAAATCGAAGCA
+ACA-GATAAC-------GGTACTGACTTCT--------------------
+ACAAAATA-TACAGTGGCAAAAGTAACAA-------------------CA
+ACAAAACC-TACAACATGAAGAGTGACCGG--------------ATCGCA
+ACAAAGTA-TACAGCCTGAAGAGCAACAG---------------------
+
+--AAAAGAGAAA-AAGGCCC---TAATAATA------CTGCCAACAG-TT
+--AAAAGAGAGA-AAGGCCC---TAATAATA------CTGCCAACAG-TT
+AGAAAGAAGAGATAAGGTTTATGTAAAGAAAGAGTCTCTCTCGAAAGCTT
+-------------------------------------TCGTCAA------
+GCGGCGCCAACGAGGGC-CCGGGCAAC------AACGTCCGGGTGAA---
+GCGAGGCAGACCGCCACACCTGCTAACCCCACCAGTACCAGTGTGAGCCC
+------------------CC------------------------------
+
+CAGAA-----------ATAAAAGTTAAAGT---TGAACCAGCAGATTCTG
+CAGAA-----------GTAAAAGTT---------GAGCTAGCAGATTCTG
+CAGAGGATG-------ATGGAAATCAAAGTG--TGAGTT--TTGACTTTA
+--------------------------------------------GTTTTA
+-AGAGGAGGCG-----GTGAAGGAGGAGGCGGGGAAACCTTCGGACGAAG
+CAGCGAAAACGCTGAGGTGAAGGAGGAGCAGGTGGAGCGCTCCGATGAAG
+-----------------CAAAGGCGG------------------------
+
+T--AGAA-------TCTTCACCCCCTTCCATTA---CCCATTCTCCACAG
+T--AGAG-------TCTTCACCCCCTTCCATTA---CCCATTCTCCACAG
+AG-AGGA-------TCTACTGCTGGTTGTGTAAACGCCAGTTTAGTACCA
+---------------CTGCTGTCCGCTCTGCCA----CTAT---------
+ACGAGGA------CTTCGACAGCAGTCCCGCC-----CCGTCCCCCGTCC
+AGGAGGAGGAGGACTCTGACAGCAGTCCCGCC-----CCGTCTCCCGGTG
+----------------CGCCATCCCTCCCGCCG----TCGTCCTCCCGCG
+
+AATG---------AATTAAAGGG---------AACAAATCA------TTC
+AATG---------AACTCAAGGG---------AACAAATCA------TTC
+GTTAC--------AACCTAGGCA---------AACACATTGCAGAGCTCC
+---------------------AA---------AACACGCCG--------C
+AGAGCGCCGGGCCGACCAAAG-GCGTTT--CCGTGGCACCCAACGCCGTG
+ACAGCGCCGGCACAGCTAAAGCGGGTTTGACTAACGCACCGAAAGAAGAA
+GCAGC---------------------------AACGCGCC----------
+
+AAA-TGAAAAAAAGAACACA-CCGGCAG-CACAGAAAAA-TAAAGTT---
+AAA-TGAAAAAAAGAACACA-CCAGCAA-CACAGAAAAA-CAAAGTT---
+ACACTGATGGAAACGATAG---CATCTA-CATAAAGTTT-TACCGCTGCC
+AA---GAGAGATGTGCTGCG-CCATCT--CTCAGACTTC-CA--------
+AAGGTGAAGGAGGCGGAGGCCCCGTCGAGCCCAAAGG---CCGCGCCG--
+GAGGAGGAGGAAGAGGAGCAGCCAGCAAGCCCAAAGGTGGCAGCGCCG--
+-------------------------------------------CGCC---
+
+--------AAACAAGACTCTGAAAGCCCTAAA--TCAACTAGTCCGTCG-
+--------AAACAGGACTCTGAAAGCCCTAAA--TCAGCTAGCCCTTCG-
+CCATCTGCAGATATGAGTC---ACGGCGTAAACGTGATGTAATTCGCCAT
+-----------CAAGA-------------AGA--------AATCC-----
+-----------TCGTTGTCGGC---------------CGCCGCCAT----
+-----------CCGCCGTCCGCTTCCCGTGCGGACAACGGCGCCACTGG-
+-----------TCG------------------------GGAGCTTC----
+
+GCTGCAGGTGGCCAGCAAAAAACC----AGAAAACCA---AAACTTTCAG
+GCTGCAGGTGGCCAGCAAAAAACC----AGGAAACCA---AAACTTTCAG
+ATCACAG-TGGTGCACAAGAAGTCGTCGAGGTATCTGGCTAAAGTCATGC
+-TTGTACTTG---AGCAAGA--TC--------------------TCCCAG
+------CCT---CCCCAAAACCAC---------------CAAACTGTCGG
+---CAACCTGGCTGCCAAAATATC---------------CAAACTGTCGG
+-------CT-----CAAAAATGAG---------------CAAACTGTCGG
+
+CTGGCTTTGACT-TTAAGCAACTTTACTGTAAACTTTGTAAACGTCAGTT
+CTGGCTTTGACT-TTAAGCAACTTTACTGTAAACTCTGTAAACGCCAGTT
+CTGCCTTGGAGAACCAGGCAG--TTA--AGAAAC-CGGCTGATGCTATCT
+TCG--CTGGAGGACTATTCAA--TCA--AGAAGC-CAGCGGATGTTGTGT
+TGGGCTTTGACT-TCAAGCAGCTCTTCTGCAAGCTGTGCAAGCGGCAGTT
+TGGGTTTTGACT-TGGAGCAGCTCTTCTGCAAGCTCTGCAAACGGCAGTT
+TGGGTTTCGACT-TCAAGCAGCTCTACTGCAAACTTTGCAAGCGTCAGTT
+
+TA--CTTC-CAAACAGAACTTGACTAAACACATCGAGTTGCACACAGATG
+TA--CTTC-CAAGCAGAACTTGACTAAACACATTGAGTTGCACACAGATG
+TGAGCAGCGCAAGCAAGA---AAATAAATGCA--AAGGAGGATGGCAGTG
+TG---------AGCAAGG-----ATCTGTCCA--AAGATCGAGATCAACA
+CAGCTCGC---GGCAGAACCTCACGAAACACATCGAGCTGCACACGGACG
+CAGCTCCC---GTCAGAATCTGACCAAGCACATCGAGCTCCACACCGACG
+CAGCTCGC---GGCAGAATCTGACCAAACACATCGAGCTGCACACGGACG
+
+GAAATAACATTTATGTTAAATTCTACAAGTGTCCTCT--TTG-CACTTAT
+GAAATAACATTTATGTTAAGTTCTACAAGTGTCCTCT--CTG-CACTTAC
+GGAA--GCATAAAACACAAGATCCACCAGCCTCCCCTAGCAGTCGCCAAC
+GGAGT----TAAAAGCTAA---CTCCAAGCATGCTT-------CGCCA--
+GCAACGACATCTTCATCAAGTTCTACCGCTGCCCCCT--CTGCCGCTA-C
+GCAACGACATCTTCATCAAGTTCTACCGCTGTCCTCT--CTGCCGCTA-C
+GCAACGACATCTTCATCAAGTTCTACCGCTGCCCTCT--CTGTCGCTA-C
+
+GAAACTCGTCGGAAACGTGATGTGATACGACATATAACTGTGGTTCATAA
+GAAACCCGTCGGAAACGTGATGTGATAAGACATATAACTGTGGTTCATAA
+AAGATCTTTTAG------TATCTCCCAAAGCAAAGAAACAGGAATCACAA
+------------------TACGTGACACG--AAAGAACC-TGA--CGAAA
+GAGTCGCGGCGCAAGCGTGACGTCCTGCGCCACGTCACGGTGGTCCACAA
+GAGTCCCGCCGCAAGCGCGACGTCCTGCGCCACGTGACCGTCGTTCACAA
+GAGTCGCGCCGCAAACGCGACGTCCTGCGCCACGTCACGGTCGTCCACAA
+
+AAAGTCATCTCGTTATCTTGGGAAAATAACAGCCAGTTTAGAGATCAGAG
+AAAGTCATCTCGTTACCTTGGGAAAATCACAGCCAGTTTAGAGATCAGAG
+A----CATCCCCTAACACTCGAAAG----CATTCCGCTTTAACATCA---
+ACAG-CACTGCGCAAC------AAG---------ACCTTAAAGACTGG--
+GAAGACCTCGGCGTACCTCGGGAAGATCATGCCCAAGCTGGAAAGCCGGG
+GAAGTCCTCCACGTACCTGGCCAAGATCATGCCCAAACTGGAGAGCCGGG
+GAAGTCCTCGGCTTACCTCGCCAAGATCATGCCCAAGCTGGAGAGCAGGG
+
+CTATAAAAAAGCCTA--TTGATTTT--GTTCTAAATAAAGT---------
+CTATAAAAAAGCCTA--TTGATTTT--GTTCTAAACAAAGT---------
+CT-TAACACCGGCAAACTTGAGTCTCCGCTTGCACCAAACA---------
+---TAATAAGGTGCA--------------CCACAAAAAGGA---------
+CGGTGAAGAGGCTCG--CCGAGGCC--GTCCTCAACAGCAC---------
+CGGTGAAGCGGCTGG--CCGAGGTG--GTCCTCAGCAGC-----------
+CGGTGAAGAGGCTGG--CGGAGGTG--GTCCTCAGCAGCACCAGCGCCAC
+
+-GGC-------AAAAAGAGGCCCTT-------------------------
+-GGC-------AAAAAGAGGCCCTT-------------------------
+-GAC-------AAGACAAGAACCTT-------------------------
+-AGT-------GAAAAAAG-------------------------------
+-GTC---CCCGAACAAGAGGCC----------------------------
+--TC---C---AACAAGAGGAC----------------------------
+CGTCACTCGCAAGCAGGAGGGCTCCGCGGCGACCCCGTCCGCCTCCGCAG
+
+----------------------------------------CGAGGGATGA
+----------------------------------------CAAGGGAGGA
+----------------------------------------CAAGCTGCCA
+--------------------------------------------------
+-----------------------------------------GAGCGGCGG
+-----------------------------------------GAGCAGCAA
+CCTGCTCCTCGTCCTCGCAGGTCCCCTCAACCGCCACTCGCAAGCAGCAG
+
+----------------------------------------------AGCA
+----------------------------------------------AGCA
+----------------------------------------------AG-A
+--------------------------------------------------
+----CGTCA-------------------------------------AGGA
+----CGGCA-------------------------------------ACCA
+GACCCGTCATCGCCCACGGTCCCGGCGTCCACGCCCGTCACCCGTAAGCA
+
+AAACATA-GTGATTCAAAA---CATGATGGCACTTCTAACTCTCCTAGTA
+AAACATA-ATGACTCAAAA---CAGGATGGCACTTCCAATTCTCCAAGTA
+ATCCACATGTCACTCGAAGT--CATAATGTTATCAAGGGACCACCCATCA
+--------------CGAAG---CCTGATAGC------------CCCA---
+GGAG-GTGAACGGGCGC-----CACGTGTCCTC--GTCCTCCTCGTCCTC
+GGCC-CCCAACACCCGCAG--GCACGAGTCCGG--ATC------------
+GGAGAGACAGCAGACGCAGCTGCACCGGCCCCTCAGCCCGCCGCTCACTC
+
+AAAAGTATGA--------------------------------AGT-AGCT
+AAAAGTATGA--------------------------------AGT-AGCC
+CCA-----GA--------------------------------AGTCAGGA
+--------------------------------------------------
+CTCCCCCTCG-------------------------------CCGCCCGTC
+-------TGA-------------------------------CAGCAGGGC
+GCCGCAGTGAAAAGCACCAGCGCAGTTGCTCCCGCGCCGCCTCGCCCGGC
+
+GACGTCG-------------------------------------------
+GACGTCG-------------------------------------------
+GACTT---------------------------------------------
+--------------------------------------------------
+ACCCCC--------------------------------------------
+GTC--C--------------------------------------------
+GCCCACACGCCACACACGCGGCGCCATGACGCCCAGTCAGACGGTGGCGG
+
+--------GTATTGAAGTAAAAGTCACAAAAAACTTTTCTCTTCACAGAT
+--------GTATTGAAGTGAAAGTCACAAAAAACTTTTCTCTTCACAGAT
+--------GTACTGAGGTTAGAGTAACCAAAAACTTTTCCCTCCATGCGT
+--------------AAGGCAGTGTCACCAAGAAAT---CAGTGCATGTGT
+-------TCCACCGAAGTCAGAGTGACCAAGAACTTCTCCCTCCATGCCT
+-------TCCACCGAAGTCAAAGTGACGAAAAACTTCTCCCTGCATGCGT
+GACGTCGTCCACTGAGGTCAGGGTGACCAAGAACTTCTCGCTGCACGCCT
+
+GCAATAAATGTGGAAAGGCATTTGCCAAAAAGACTTACCTTGA-ACATCA
+GCAATAAATGTGGAAAGGCATTTGCCAAAAAGACTTACCTTGA-ACATCA
+GCGATATGTGTGGCAGAGCATTTGCCAAAAAGGTTTACCTTGAGACA-CA
+GTGACGTCTGTGGGGAGAGCTTCATGAAGACAAGGTATCTGGG-GTTGCA
+GCGACCAGTGTGGACGGGCCTTTGCCAAGAAGCTGTACCTGGA-GTCTCA
+GCGATCAGTGTGGGCGGGCCTTCGCCAAGAAGCTTTATTTGGA-ATCTCA
+GCGACCAGTGCGGACGCGCCTTCGCCAAAAAGCTGTATCTGGA-GTCTCA
+
+TAAGAAAACTCATAAGGCAAATGCTTCCAATTCACCTGAAGGAAACAAAA
+TAAGAAAACTCATAAGGCAAATGCTACCAATTCACCTGAAGGAAACAAAA
+CAGGCGGAGACACAAGAC---TGCCATTG------CTAGTGGGGACAAAT
+CAAGAGAATGCATCTGAAAACCGCATCCA------------GGAGCG---
+CAAGCGCAGTCATCGCAACGCGGCGACGG------CGGCGGCCAGCAGGA
+CAAGCGAAGTCATCGGAACGCGGCGGTGG------CGGCAGCCAGCAGGA
+CAAGCGCAGCCATCGCAACGCACCAACCG------CAGCGGCTAACAGGC
+
+CCAAAGGCCGAAGTACAAGATCTAAGGCTCTTGTCTGA
+CCAAAGGCCGAAGTACAAGATCTAAGGCTCTTGTCTGA
+TACAAGGAAGAAGCACTCGATCAAAGGCTCTCATTTGA
+CAGGAGTCAGAA---CTAGGTCAAAGGCCATGCTTTGA
+GGAAAGGAGTCAGCACCCGCTCCAAGTCCCTGGTC---
+GGAAAGGTGTCAGCACGCGCTCCAAGTCCCTGATG---
+GCAAGGGAGTCAGCACCCGCTCCAAGACCCTGGCC---;
+end;
+
diff --git a/debian/phyml.examples b/debian/phyml.examples
index e39721e..dd1d6f3 100644
--- a/debian/phyml.examples
+++ b/debian/phyml.examples
@@ -1 +1,2 @@
 examples/*
+debian/phyml-examples/*
diff --git a/debian/tests/run-unit-test b/debian/tests/run-unit-test
index 32b94b5..656be61 100644
--- a/debian/tests/run-unit-test
+++ b/debian/tests/run-unit-test
@@ -20,6 +20,6 @@ echo "AA interleaved sequence file, default parameters :"
 /usr/bin/phyml -i proteic -d aa
 
 echo "AA sequential sequence file, with customization :"
-/usr/bin/phyml -i nexus_example.nxs -q -d aa -m JTT -c 4 -a e
+/usr/bin/phyml -i example.nex -d nt -c 4 -a e
 
 echo "PASS"

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/phyml.git

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