"Populations" version 1.2.21 is a population genetic software working on gene frequencies. It computes distances (including microsatellites based distances) between individuals or populations, makes phylogenetic trees (NJ or UPGMA) and bootstraps on locus or individuals. It is also usefull to convert data files: Genepop, genetix, msat...

it works with linux or windows (but it's better on linux ;-)). You can download it from:
http://www.pge.cnrs-gif.fr/bioinfo/populations/index.php?lang=en

let me know about your experience using Populations:
Olivier.Langella[at]pge.cnrs-gif.fr

thanks,
Olivier