[med-svn] [examl] 01/02: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
in repository examl.

commit f38325e60b5a3a1792f36eb69d77ab91991edf32
Author: Andreas Tille <tille at debian.org>
Date:   Wed Feb 15 17:29:07 2017 +0100

    Add manpage
---
 debian/examl.1  | 161 ++++++++++++++++++++++++++++++++++++++++++++++++++++++++
 debian/links    |   4 +-
 debian/manpages |   1 +
 3 files changed, 165 insertions(+), 1 deletion(-)

diff --git a/debian/examl.1 b/debian/examl.1
new file mode 100644
index 0000000..e6b33da
--- /dev/null
+++ b/debian/examl.1
@@ -0,0 +1,161 @@
+.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
+.TH EXAML "1" "February 2017" "examl 3.0.18" "User Commands"
+.SH NAME
+examl \- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference
+examl-AVX \- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using AVX
+examl-OMP \- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using OMP
+examl-OMP-AVX \- Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using AVX and OMP
+.SH SYNOPSIS
+.B examl|examl\-AVX|examl\-OMP|examl\-OMP\-AVX
+\fB\-s\fR binarySequenceFileName
+\fB\-n\fR outputFileNames
+\fB\-m\fR rateHeterogeneityModel
+\fB\-t\fR userStartingTree|\-R binaryCheckpointFile|\-g constraintTree \fB\-p\fR randomNumberSeed
+[\-a]
+[\-B numberOfMLtreesToSave]
+[\-c numberOfCategories]
+[\-D]
+[\-e likelihoodEpsilon]
+[\-f d|e|E|o|q]
+[\-h]
+[\-i initialRearrangementSetting]
+[\-I quartetCheckpointInterval]
+[\-M]
+[\-r randomQuartetNumber]
+[\-S]
+[\-v]
+[\-w outputDirectory]
+[\-Y quartetGroupingFileName]
+[\-\-auto\-prot=ml|bic|aic|aicc]
+.SH OPTIONS
+.TP
+\fB\-a\fR
+use the median for the discrete approximation of the GAMMA model of rate heterogeneity
+.IP
+DEFAULT: OFF
+.TP
+\fB\-B\fR
+specify the number of best ML trees to save and print to file
+.TP
+\fB\-c\fR
+Specify number of distinct rate catgories for ExaML when modelOfEvolution
+is set to GTRPSR
+Individual per\-site rates are categorized into numberOfCategories rate
+categories to accelerate computations.
+.IP
+DEFAULT: 25
+.TP
+\fB\-D\fR
+ML search convergence criterion. This will break off ML searches if the relative
+Robinson\-Foulds distance between the trees obtained from two consecutive lazy SPR cycles
+is smaller or equal to 1%. Usage recommended for very large datasets in terms of taxa.
+On trees with more than 500 taxa this will yield execution time improvements of approximately 50%
+While yielding only slightly worse trees.
+.IP
+DEFAULT: OFF
+.TP
+\fB\-e\fR
+set model optimization precision in log likelihood units for final
+optimization of model parameters
+.IP
+DEFAULT: 0.1
+.TP
+\fB\-f\fR
+select algorithm:
+.TP
+"\-f d": new rapid hill\-climbing
+DEFAULT: ON
+.IP
+"\-f e": compute the likelihood of a bunch of trees passed via \fB\-t\fR
+.IP
+this option will do a quick and dirty optimization without re\-optimizng
+the model parameters for each tree
+.IP
+"\-f E": compute the likelihood of a bunch of trees passed via \fB\-t\fR
+.IP
+this option will do a thorough optimization that re\-optimizes
+the model parameters for each tree
+.IP
+"\-f o": old and slower rapid hill\-climbing without heuristic cutoff
+.IP
+"\-f q": fast quartet calculator
+.IP
+DEFAULT for "\-f": new rapid hill climbing
+.TP
+\fB\-g\fR
+Pass a multi\-furcating constraint tree to ExaML. The tree needs to contain all taxa of the alignment!
+When using this option you also need to specify a random number seed via "\-p"
+.TP
+\fB\-h\fR
+Display this help message.
+.TP
+\fB\-i\fR
+Initial rearrangement setting for the subsequent application of topological
+changes phase
+.TP
+\fB\-I\fR
+Set after how many quartet evaluations a new checkpoint will be printed.
+.IP
+DEFAULT: 1000
+.TP
+\fB\-m\fR
+Model of rate heterogeneity
+.IP
+select "\-m PSR" for the per\-site rate category model (this used to be called CAT in RAxML)
+select "\-m GAMMA" for the gamma model of rate heterogeneity with 4 discrete rates
+.TP
+\fB\-M\fR
+Switch on estimation of individual per\-partition branch lengths. Only has effect when used in combination with "\-q"
+Branch lengths for individual partitions will be printed to separate files
+A weighted average of the branch lengths is computed by using the respective partition lengths
+.IP
+DEFAULT: OFF
+.TP
+\fB\-n\fR
+Specifies the name of the output file.
+.TP
+\fB\-p\fR
+Specify a random number seed, required in conjunction with the "\-g" option for constraint trees
+.TP
+\fB\-R\fR
+read in a binary checkpoint file called ExaML_binaryCheckpoint.RUN_ID_number
+.TP
+\fB\-r\fR
+Pass the number of quartets to randomly sub\-sample from the possible number of quartets for the given taxon set.
+Only works in combination with \fB\-f\fR q !
+.TP
+\fB\-s\fR
+Specify the name of the BINARY alignment data file generated by the parser component
+.TP
+\fB\-S\fR
+turn on memory saving option for gappy multi\-gene alignments. For large and gappy datasets specify \fB\-S\fR to save memory
+This will produce slightly different likelihood values, may be a bit slower but can reduce memory consumption
+from 70GB to 19GB on very large and gappy datasets
+.TP
+\fB\-t\fR
+Specify a user starting tree file name in Newick format
+.TP
+\fB\-v\fR
+Display version information
+.TP
+\fB\-w\fR
+FULL (!) path to the directory into which ExaML shall write its output files
+.IP
+DEFAULT: current directory
+.TP
+\fB\-Y\fR
+Pass a quartet grouping file name defining four groups from which to draw quartets
+The file input format must contain 4 groups in the following form:
+(Chicken, Human, Loach), (Cow, Carp), (Mouse, Rat, Seal), (Whale, Frog);
+Only works in combination with \fB\-f\fR q !
+.HP
+\fB\-\-auto\-prot\fR=\fI\,ml\/\fR|bic|aic|aicc When using automatic protein model selection you can chose the criterion for selecting these models.
+.IP
+RAxML will test all available prot subst. models except for LG4M, LG4X and GTR\-based models, with and without empirical base frequencies.
+You can chose between ML score based selection and the BIC, AIC, and AICc criteria.
+.IP
+DEFAULT: ml
+.SH AUTHOR
+Alexandros Stamatakis, Andre J. Aberer, and Alexey Kozlov on February 14 2017.
+.PP
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.
diff --git a/debian/links b/debian/links
index d9b57b6..479a682 100644
--- a/debian/links
+++ b/debian/links
@@ -1,4 +1,6 @@
 usr/lib/examl/bin/examl-AVX	usr/bin/examl-AVX
 usr/lib/examl/bin/examl-OMP	usr/bin/examl-OMP
 usr/lib/examl/bin/examl-OMP-AVX	usr/bin/examl-OMP-AVX
-
+usr/share/man/man1/examl.1.gz	usr/share/man/man1/examl-AVX.1.gz
+usr/share/man/man1/examl.1.gz	usr/share/man/man1/examl-OMP.1.gz
+usr/share/man/man1/examl.1.gz	usr/share/man/man1/examl-OMP-AVX.1.gz
diff --git a/debian/manpages b/debian/manpages
new file mode 100644
index 0000000..0f65186
--- /dev/null
+++ b/debian/manpages
@@ -0,0 +1 @@
+debian/*.1

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