[med-svn] [prottest] 06/06: Add manpage

[Andreas Tille]

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tille pushed a commit to branch master
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commit 497df3fca340905dd6b41407f1fa7bcb3115a04b
Author: Andreas Tille <tille at debian.org>
Date:   Mon Oct 19 15:23:29 2015 +0200

    Add manpage
---
 debian/manpages   |   1 +
 debian/prottest.1 | 131 ++++++++++++++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 132 insertions(+)

diff --git a/debian/manpages b/debian/manpages
new file mode 100644
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--- /dev/null
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+debian/*.1
diff --git a/debian/prottest.1 b/debian/prottest.1
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+.TH PROTTEST "1" "October 2015" "prottest 3.4" "User Commands"
+.SH NAME
+prottest \- Selection of best-fit models of protein evolution (sequential version)
+.SH SYNOPSIS
+.B prottest
+\fB\-i\fR alignm_file [OPTIONS]
+
+.SH DESCRIPTION
+ PROTTEST (ModelTest's relative) is a program for selecting the model of
+ protein evolution that best fits a given set of sequences (alignment).
+ This java program is based on the Phyml program (for maximum likelihood
+ calculations and optimization of parameters) and uses the PAL library as
+ well. Models included are empirical substitution matrices (such as WAG,
+ LG, mtREV, Dayhoff, DCMut, JTT, VT, Blosum62, CpREV, RtREV, MtMam,
+ MtArt, HIVb, and HIVw) that indicate relative rates of amino acid
+ replacement, and specific improvements (+I:invariable sites, +G: rate
+ heterogeneity among sites, +F: observed amino acid frequencies) to
+ account for the evolutionary constraints impossed by conservation of
+ protein structure and function. ProtTest uses the Akaike Information
+ Criterion (AIC) and other statistics (AICc and BIC) to find which of the
+ candidate models best fits the data at hand.
+.SH OPTIONS
+.HP
+\fB\-i\fR alignment_filename
+.IP
+Alignment input file (required)
+.HP
+\fB\-t\fR tree_filename
+.IP
+Tree file (optional) [default: NJ tree]
+.HP
+\fB\-o\fR output_filename
+.IP
+Output file (optional) [default: standard output]
+.HP
+\fB\-log\fR enabled/disabled
+.IP
+Enables / Disables PhyML logging into log directory (see prottest.properties)
+.HP
+\fB\-[matrix]\fR
+.IP
+Include matrix (Amino\-acid) = JTT LG DCMut MtREV MtMam MtArt Dayhoff WAG
+RtREV CpREV Blosum62 VT HIVb HIVw FLU
+.IP
+If you don't specify any matrix, all matrices displayed above will
+be included.
+.HP
+\fB\-I\fR
+.IP
+Include models with a proportion of invariable sites
+.HP
+\fB\-G\fR
+.IP
+Include models with rate variation among sites and number of categories
+.HP
+\fB\-IG\fR
+.IP
+include models with both +I and +G properties
+.HP
+\fB\-all\-distributions\fR
+.IP
+Include models with rate variation among sites, number of categories and both
+.HP
+\fB\-ncat\fR number_of_categories
+.IP
+Define number of categories for +G and +I+G models [default: 4]
+.HP
+\fB\-F\fR
+.IP
+Include models with empirical frequency estimation
+.HP
+\fB\-AIC\fR
+.IP
+Display models sorted by Akaike Information Criterion (AIC)
+.HP
+\fB\-BIC\fR
+.IP
+Display models sorted by Bayesian Information Criterion (BIC)
+.HP
+\fB\-AICC\fR
+.IP
+Display models sorted by Corrected Akaike Information Criterion (AICc)
+.HP
+\fB\-DT\fR
+.IP
+Display models sorted by Decision Theory Criterion
+.HP
+\fB\-all\fR
+.IP
+Displays a 7\-framework comparison table
+.HP
+\fB\-S\fR optimization_strategy
+.IP
+Optimization strategy mode: [default: 0]
+.IP
+0: Fixed BIONJ JTT
+.IP
+1: BIONJ Tree
+.IP
+2: Maximum Likelihood tree
+.IP
+3: User defined topology
+.HP
+\fB\-s\fR moves
+.IP
+Tree search operation for ML search:
+NNI (fastest), SPR (slowest), BEST (best of NNI and SPR) [default: NNI]
+.HP
+\fB\-t1\fR                                    
+.IP
+Display best\-model's newick tree [default: false]
+.HP
+\fB\-t2\fR                                    
+.IP
+Display best\-model's ASCII tree
+[default: false]
+.HP
+\fB\-tc\fR consensus_threshold
+.IP
+Display consensus tree with the specified threshold, between 0.5 and 1.0
+[0.5 = majority rule consensus ; 1.0 = strict consensus]
+.HP
+\fB\-threads\fR number_or_threads                     
+.IP
+Number of threads requested to compute (only if MPJ is not used) [default: 1]
+.HP
+\fB\-verbose\fR
+.IP
+Verbose mode [default: false]
+.SH EXAMPLE
+prottest \fB\-i\fR alignm_file \fB\-t\fR tree_file \fB\-S\fR 0 \fB\-all\-distributions\fR \fB\-F\fR \fB\-AIC\fR \fB\-BIC\fR \fB\-tc\fR 0.5 > output

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