It should be possibly to code the data numerical, treating the loci as characters and the alleles as character stats. The data matrix can then be analyzed using distance methods or parsimony. But I have no idea how useful the results will be.

You could generate genetic distances from your geneotypes (populations or individuals) and construct a Neighbor-Joining tree. Alternatively, there is some newish software called "Neighbor-Net" that constructs "Phylogenetic Networks" but it may only use sequence data.

Hello. You can do a neighbor-joining tree based on Nei's standard distances derived from microsatellite allele frequencies.

Take a look at the Populations software (http://bioinformatics.org/populations/). It should do what you need.

You can use the "old" software package PHYLIP (http://evolution.gs.washington.edu/phylip.html). There is also a Facebook page for discussions (https://www.facebook.com/pages/PHYLIP/115402811804635).

There are several ways. The easiest is just to run Arlequin- get the distance matrix of your choice and use phylip to make a NJ tree; you may also use MEGA instead of phylip for a better visualisation.

If you are good in R, then can use ape package and draw NJ tree

http://cran.r-project.org/web/packages/ape/index.html

As suggested Andrew, Population software could be used for individuals/populaitons distances and trees based on microsatellite data. You can use the Genepop formate as infile.

I agree with Andrew, I also used Populations software by adding my data in GenePop formate.

may you send me the link to Population software to download it please !

Here is the link:

http://bioinformatics.org/~tryphon/populations/#ancre_telechargement

Could somebody tell me how to use the populations software to draw the NJ tree microstellite data? I tried it in the command line with a Genepop input file but it is not working. Is there any manual or documentation for the software?