---
name: "populations"
section: "1"
platform: "linux"
package: "populations"
version: "1.2.33+svn0120106+dfsg-7"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/populations"
---

# populations(1)

population genetic software

## NAME

populations - population genetic software

## SYNOPSIS

**populations**

**populations** \[*name\_of\_input\_file*\] \[*option*\]

You can use **populations** as a command line program (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)

## AUTHOR

**Georges Khaznadar** \<georgesk@ofset.org\>

Wrote this manpage for the Debian system.

## COPYRIGHT

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.