populations(1) [debian man page]
POPULATIONS(1) populations User Manual POPULATIONS(1) NAME
populations - population genetic software SYNOPSIS
populations populations [name_of_input_file] [option] You can use populations as a command line programm (very useful for batch treatment) to infer phylogenetic trees. DESCRIPTION
populations is a population genetic software. It computes genetic distances between populations or individuals. It builds phylogenetic trees (NJ or UPGMA) with bootstrap values. FEATURES
o haploids, diploids or polyploids genotypes (see input formats) o structured populations (see input files structured populations o No limit of populations, loci, alleles per loci (see input formats) o Distances between individuals (15 different methods) o Distances between populations (15 methods) o Bootstraps on loci OR individuals o Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format) o Allelic diversity o Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...) OPTIONS
-phylogeny ind|pop (default) for phylogenetic trees based on individuals or populations dist method (default: Nei standard, Ds) you can choose among: DAS, Dm, Ds, Dc, Da, dmu2, Fst, Cp, Dr, ASD, Dsw, Dr, Dru, Drw, Drl. see distances for details. -construct method (default: upgma) possibilities upgma or nj (Neighbor Joining) -bootstrap_ind n number to indicate the number of bootstraps to perform on individuals -bootstrap_locus n number to indicate the number of bootstraps to perform on loci .RE -output name_of_treeview_file to indicate the name of the tree file (phylip tree format) -level n number , structured populations allows to choose the structuration factor (in the example: town level is 1, building level is 2...). EXAMPLE
populations toutc2.txt -phylogeny pop -dist Dm -bootstrap_locus 10000 -output toutc2_10000_Dm.tre Commands can be write in a .bat file (for DOS) or a script file (for UNIX) AUTHOR
Georges Khaznadar <georgesk@ofset.org> Wrote this manpage for the Debian system. COPYRIGHT
Copyright (C) 2011 Georges Khaznadar This manual page was written for the Debian system (and may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL. populations 06/19/2011 POPULATIONS(1)
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JSDOC-TOOLKIT(1) jsdoc-toolkit User Manual JSDOC-TOOLKIT(1) NAME
jsdoc - automatic generator for HTML documentation of Javascript sources SYNOPSIS
jsdoc {-d=<PATH> | --directory=<PATH>} [options] <SRC_DIR_OR_FILE> ... jsdoc [{-h | --help}] DESCRIPTION
This manual page documents briefly the jsdoc command. jsdoc is application, written in JavaScript, for automatically generating template-formatted, multi-page HTML (or XML, JSON, or any other text-based) documentation from commented JavaScript source code. OPTIONS
The program follows the usual GNU command line syntax, with long options starting with two dashes (`-'). A summary of options is included below. For a complete description, see the info(1) files. -a, --allfunction Include all functions, even undocumented ones. -c, --conf Load a configuration file. -d=<PATH>, --directory=<PATH> Output to this directory (required parameter). -D="myVar:My value", --define="myVar:My value" Multiple. Define a variable, available in JsDoc as JSDOC.opt.D.myVar. -e=<ENCODING>, --encoding=<ENCODING> Use this encoding to read and write files. -E="REGEX", --exclude="REGEX" Multiple. Exclude files based on the supplied regex. -h, --help Show this message and exit. -m, --multiples Don't warn about symbols being documented more than once. -n, --nocode Ignore all code, only document comments with @name tags. -o=<PATH>, --out=<PATH> Print log messages to a file (defaults to stdout). -p, --private Include symbols tagged as private, underscored and inner symbols. -q, --quiet Do not output any messages, not even warnings. -r=<DEPTH>, --recurse=<DEPTH> Descend into src directories. -s, --suppress Suppress source code output. -S, --securemodules Use Secure Modules mode to parse source code. -t=<PATH>, --template=<PATH> Use this template to format the output. -T, --test Run all unit tests and exit. -u, --unique Force file names to be unique, but not based on symbol names. -v, --verbose Provide verbose feedback about what is happening. -x=<EXT>[,EXT]..., --ext=<EXT>[,EXT]... Scan source files with the given extension/s (defaults to js). BUGS
The following bugs are known bugs: Does not support spaces in arguments The wrapper jsdoc is not immune to spaces in filenames, either escaped or not. AUTHOR
Georges Khaznadar <georgesk@ofset.org> Wrote this manpage for the Debian system. COPYRIGHT
Copyright (C) 2011 Georges Khaznadar This manual page was written for the Debian system (and may be used by others). Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 or (at your option) any later version published by the Free Software Foundation. On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common-licenses/GPL-2. jsdoc-toolkit 07/16/2011 JSDOC-TOOLKIT(1)