A program to define the genetic structure of populations by a simulated annealing approach

Introduction Input files Running Output files Known issues References Download


SAMOVA 1.0 implements an approach to define groups of populations that are geographically homogeneous and maximally differentiated from each other. As a by-product, it also leads to the identification of genetic barriers between these groups. The method is based on a simulated annealing procedure that aims at maximizing the proportion of total genetic variance due to differences between groups of populations (SAMOVA, Spatial Analysis of MOlecular VAriance). The method is described in Dupanloup, Schneider and Excoffier (2002).

SAMOVA 1.0 runs on Windows. There is no Linux or Mac version yet.

Input files

SAMOVA 1.0 needs two input files. The first one (*.geo) must contain the geographic coordinates of the sampling localities of your populations. The second one (*.arp) is an Arlequin input file containing the genetic data sampled in your populations. The Arlequin file must have the SAME NAME as the geographical file with the extension (*.arp). The order of the populations in the two input files MUST BE THE SAME !!!

The file containing the geographic coordinates of the sampling localities of your populations must have the .geo extension.
Important notice: SAMOVA 1.0 does not work if two sampling localities have the same geographical coordinates.
The geographical input file must be structured the following way. Each line corresponds to a population. Each line must contain five fields separated by a tab character:

Examples of input files are given below:


SAMOVA needs:

When the SAMOVA window disappears from your screen that means that the computations are finished. It takes time and this time depends on the number of populations you have and the number of simulated annealing processes you wish to perform.

Output files

A set of output files are created by SAMOVA:

Known issues


See also:

Isabelle Dupanloup, CMPG, Institute of Ecology and Evolution, University of Bern