POPULATIONS(1) | populations User Manual | POPULATIONS(1) |
NAME¶
populations - population genetic softwareSYNOPSIS¶
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¶
•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
.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 © 2011 Georges Khaznadar06/19/2011 | populations |