populations(1)

Usage

populations

populations [name_of_input_file] [option]

Overview

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

• 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...)

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...).

Examples

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)

Releases

7 releases since Debian 7 (Wheezy); the text changed 1 time.