populations - Online in the Cloud

PROGRAM:

NAME

populations - population genetic software

SYNOPSIS

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
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)

Use populations online using onworks.net services