[med-svn] [jmodeltest] 03/04: Add manpage

Andreas Tille tille at debian.org
Wed Aug 17 14:12:40 UTC 2016 

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

tille pushed a commit to branch master
in repository jmodeltest.

commit df46e5bc83f0e868927f6359d32f56c79338ce76
Author: Andreas Tille <tille at debian.org>
Date:   Wed Aug 17 15:43:46 2016 +0200

    Add manpage
---
 debian/links               |   7 +-
 debian/manpages            |   1 +
 debian/runjmodeltest-gui.1 | 192 +++++++++++++++++++++++++++++++++++++++++++++
 3 files changed, 197 insertions(+), 3 deletions(-)

diff --git a/debian/links b/debian/links
index e9f1e22..232e27f 100644
--- a/debian/links
+++ b/debian/links
@@ -1,3 +1,4 @@
-usr/share/jmodeltest/jModelTest.jar	usr/share/java/jmodeltest.jar
-etc/jmodeltest				usr/share/jmodeltest/conf
-var/log/jmodeltest			usr/share/jmodeltest/log
+usr/share/jmodeltest/jModelTest.jar		usr/share/java/jmodeltest.jar
+etc/jmodeltest					usr/share/jmodeltest/conf
+var/log/jmodeltest				usr/share/jmodeltest/log
+usr/share/man/man1/runjmodeltest-gui.1.gz	usr/share/man/man1/jmodeltest.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
diff --git a/debian/runjmodeltest-gui.1 b/debian/runjmodeltest-gui.1
new file mode 100644
index 0000000..cb62af1
--- /dev/null
+++ b/debian/runjmodeltest-gui.1
@@ -0,0 +1,192 @@
+.TH JMODELTEST "1" "August 2016" "jmodeltest 2.1.10" "User Commands"
+.SH NAME
+jmodeltest \- HPC selection of models of nucleotide substitution
+.SH SYNOPSIS
+.B jmodeltest
+\fB\-d\fR sequenceFileName
+[\-getPhylip]
+[\-ckp checkpointFileName.ckp]
+[\-n executionName]
+[\-t fixed|BIONJ|ML] [\-u userTreeFileName] [\-o outputFileName]
+[\-S NNI|SPR|BEST]
+[\-AIC] [\-AICc] [\-BIC] [\-DT] [\-c confidenceInterval]
+[\-s 3|5|7|11|203]
+[\-f] [\-i] [\-g numberOfCategories]
+[\-uLNL]
+[\-dLRT] [\-h confidenceInterval] [\-hLRT] [\-O {ftvwxgp}]
+[\-a] [\-z] [\-p] [\-v] [\-w]
+[\-tr numberOfThreads] [\-machinesfile machinesFileName]
+.SH DESCRIPTION
+jModelTest is a tool to carry out statistical selection of best-fit
+models of nucleotide substitution. It implements five different model
+selection strategies: hierarchical and dynamical likelihood ratio tests
+(hLRT and dLRT), Akaike and Bayesian information criteria (AIC and BIC),
+and a decision theory method (DT). It also provides estimates of model
+selection uncertainty, parameter importances and model-averaged
+parameter estimates, including model-averaged tree topologies.
+jModelTest 2 includes High Performance Computing (HPC) capabilities and
+additional features like new strategies for tree optimization, model-
+averaged phylogenetic trees (both topology and branch length), heuristic
+filtering and automatic logging of user activity.
+.SH OPTIONS
+.HP
+\fB\-a\fR
+.IP
+estimate model\-averaged phylogeny for each active criterion (e.g., \fB\-a\fR) (default is false)
+.HP
+\fB\-AIC\fR
+.IP
+calculate the Akaike Information Criterion (e.g., \fB\-AIC\fR) (default is false)
+.HP
+\fB\-AICc\fR
+.IP
+calculate the corrected Akaike Information Criterion (e.g., \fB\-AICc\fR) (default is false)
+.HP
+\fB\-BIC\fR
+.IP
+calculate the Bayesian Information Criterion (e.g., \fB\-BIC\fR) (default is false)
+.HP
+\fB\-DT\fR
+.IP
+calculate the decision theory criterion (e.g., \fB\-DT\fR) (default is false)
+.HP
+\fB\-c\fR confidenceInterval
+.IP
+confidence interval (e.g., \fB\-c\fR 90) (default is 100)
+.HP
+\fB\-ckp\fR checkpointFileName
+.IP
+Loads a checkpointing file
+.HP
+\fB\-d\fR sequenceFileName
+.IP
+input data file (e.g., \fB\-d\fR data.phy)
+.HP
+\fB\-dLRT\fR
+.IP
+do dynamical likelihood ratio tests (e.g., \fB\-dLRT\fR)(default is false)
+.HP
+\fB\-f\fR
+.IP
+include models with unequals base frecuencies (e.g., \fB\-f\fR) (default is false)
+.HP
+\fB\-g\fR numberOfCategories
+.IP
+include models with rate variation among sites and number of categories (e.g., \fB\-g\fR 8) (default is false & 4 categories)
+.HP
+\fB\-G\fR threshold
+.IP
+heuristic search. Requires a threshold > 0 (e.g., \fB\-G\fR 0.1)
+.HP
+\fB\-getPhylip\fR
+.IP
+converts the input file into phylip format
+.HP
+\fB\-h\fR confidenceInterval
+.IP
+confidence level for the hLRTs (e.g., \fB\-a0\fR.002) (default is 0.01)
+.HP
+\fB\-H\fR informationCriterion
+.IP
+information criterion for clustering search (AIC, AICc, BIC). (default is BIC)
+this argument applies only for 203 substitution schemes (e.g., \fB\-s\fR 203 \fB\-H\fR AIC)
+.HP
+\fB\-help\fR
+.IP
+displays this help message
+.HP
+\fB\-hLRT\fR
+.IP
+do hierarchical likelihood ratio tests (default is false)
+hypothesis testing order can be specified with \fB\-O\fR argument
+.HP
+\fB\-i\fR
+.IP
+include models with a proportion invariable sites (e.g., \fB\-i\fR) (default is false)
+.HP
+\fB\-machinesfile\fR manchinesFileName
+.IP
+gets the processors per host from a machines file
+.HP
+\fB\-n\fR executionName
+.IP
+execution name for appending to the log filenames (default: current time yyyyMMddhhmmss)
+.HP
+\fB\-o\fR outputFileName
+.IP
+set output file (e.g., \fB\-o\fR jmodeltest.out)
+.HP
+\fB\-O\fR hypothesisOrder
+.IP
+hypothesis order for the hLRTs (e.g., \fB\-hLRT\fR \fB\-O\fR gpftv) (default is ftvwxgp)
+.IP
+f=freq, t=titvi, v=2ti4tv(subst=3)/2ti(subst>3), w=2tv, x=4tv, g=gamma, p=pinv
+this argument is used only if \fB\-hLRT\fR argument is set
+\&'f','t','v','g','p' are mandatory in any order. 'w' is optional, and 'x' requires 'w' to be present
+thus, length should be 5, 6 *including 'w') or 7 (including both 'w' and 'x')
+e.g., \fB\-hLRT\fR \fB\-O\fR gpfvwxt
+.HP
+\fB\-p\fR
+.IP
+calculate parameter importances (e.g., \fB\-p\fR) (default is false)
+.HP
+\fB\-r\fR
+.IP
+backward selection for the hLRT (e.g., \fB\-r\fR) (default is forward)
+.HP
+\fB\-s\fR numberOfSubstitutionSchemes
+.IP
+number of substitution schemes (e.g., \fB\-s\fR 11) (it has to be 3,5,7,11,203; default is 3)
+.HP
+\fB\-\-set\-local\-config\fR localConfigurationFile
+.IP
+set a local configuration file in replacement of conf/jmodeltest.conf
+.HP
+\fB\-\-set\-property\fR propertyName=propertyValue
+.IP
+set a new value for a property contained in the configuration file (conf/jmodeltest.conf)
+.HP
+\fB\-S\fR NNI|SPR|BEST
+.IP
+tree topology search operation option (NNI (fast), SPR (a bit slower), BEST (best of NNI and SPR)) (default is BEST)
+.HP
+\fB\-t\fR fixed|BIONJ|ML
+.IP
+base tree for likelihood calculations (e.g., \fB\-t\fR BIONJ)
+.IP
+fixed  (common BIONJ\-JC topology)
+.IP
+BIONJ  (Neighbor\-Joining topology)
+.IP
+ML     (Maximum Likelihood topology) (default)
+.HP
+\fB\-tr\fR numberOfThreads
+.IP
+number of threads to execute (default is 4)
+.HP
+\fB\-u\fR treeFileName
+.TP
+user tree for likelihood calculations
+(e.g., \fB\-u\fR data.tre)
+.HP
+\fB\-uLnL\fR
+.IP
+calculate delta AIC,AICc,BIC against unconstrained likelihood (e.g., \fB\-uLnL\fR)
+.IP
+(default is false if the input alignment has gaps or ambiguous characters)
+.HP
+\fB\-v\fR
+.IP
+do model averaging and parameter importances (e.g., \fB\-v\fR) (default is false)
+.HP
+\fB\-w\fR
+.IP
+write PAUP block (e.g., \fB\-w\fR) (default is false)
+.HP
+\fB\-z\fR
+.IP
+strict consensus type for model\-averaged phylogeny (e.g., \fB\-z\fR) (default is majority rule)
+.SH EXAMPLE
+jmodeltest \fB\-d\fR sequenceFileName \fB\-i\fR \fB\-f\fR \fB\-g\fR 4 \fB\-BIC\fR \fB\-AIC\fR \fB\-AICc\fR \fB\-DT\fR \fB\-v\fR \fB\-a\fR \fB\-w\fR
+.SH AUTHOR
+This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

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