populations - population genetic software

GeorgesKhaznadar <georgesk@ofset.org>
           Wrote this manpage for the Debian system.

       Copyright © 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)

populations is a population genetic software. It computes genetic distances between populations or
       individuals. It builds phylogenetic trees (NJ or UPGMA) with bootstrap values.

populationstoutc2.txt-phylogenypop-distDm-bootstrap_locus10000-outputtoutc2_10000_Dm.tre

       Commands can be write in a .bat file (for DOS) or a script file (for UNIX)

       •   haploids, diploids or polyploids genotypes (see input formats)

       •   structured populations (see input files structured populations

       •   No limit of populations, loci, alleles per loci (see input formats)

       •   Distances between individuals (15 different methods)

       •   Distances between populations (15 methods)

       •   Bootstraps on loci OR individuals

       •   Phylogenetic trees (individuals or populations), using Neighbor Joining or UPGMA (PHYLIP tree format)

       •   Allelic diversity

       •   Converts data files from Genepop to different formats (Genepop, Genetix, Msat, Populations...)

       populations - population genetic software

-phylogenyind|pop
           (default) for phylogenetic trees based on individuals or populations

       distmethod
           (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.

       -constructmethod
           (default: upgma) possibilities upgma or nj (Neighbor Joining)

       -bootstrap_indn
           number to indicate the number of bootstraps to perform on individuals

       -bootstrap_locusn

           number to indicate the number of bootstraps to perform on loci
                 .RE

           -outputname_of_treeview_file
               to indicate the name of the tree file (phylip tree format)

           -leveln
               number , structured populations allows to choose the structuration factor (in the example: town
               level is 1, building level is 2...).

populationspopulations [name_of_input_file] [option]

       You can use populations as a command line program (very useful for batch treatment) to infer phylogenetic
       trees.