- populations [name_of_input_file] [option]
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...)
- (default) for phylogenetic trees based on individuals or populations
- (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.
- (default: upgma) possibilities upgma or nj (Neighbor Joining)
- number to indicate the number of bootstraps to perform on individuals
number to indicate the number of bootstraps to perform on loci
- to indicate the name of the tree file (phylip tree format)
- 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.