populations (1)

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.

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

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...)

-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...).

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)

Georges Khaznadar <[email protected]>

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.