Dear colleagues, I would like to thank to the many who have answered. I have received more than 20 answers in more than 2 days. My big thanks. So that others can use the information sent to me and for future reference, here it is a summary of the answers. The biggest suggestion seemed to fall to the Nexus file format. PHYLIP and LAMARC formats were also referred quite a lot. Also MIGRATE-N. Other references were: IBDWS, BAPS, MDIV/IM, SITES (probably a couple were forgotten, I am sorry). >From my (highly subjective) analysis Nexus and LAMARC formats will get further research. This will help extend the existing Bio.PopGen module of Biopython with a vital statistics submodule. If you are interested in coalescent simulations and selection detection, biopython might already have content that interests you, please check http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc101 Again, many thanks for all the fantastic feedback, Tiago tiagoantao@gmail.com