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)