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