I am currently developing the Biopython module for population genetics and genomics (by the way, you are invited both to help with the development and to make suggestions - maybe based on your needs - for new features).
On the current (1.44) version of Biopython, a GenoPop parser and code to deal with FDist (a Fst outlier method for selection detection) is available.
It is my pleasure to announce that coalescent simulation (in the form of support for the SimCoal2 simulator) is currently available on CVS and will probably be out on the next public version. This includes, code, test code and DOCUMENTATION. This means you can now do coalescent simulations from inside Biopython (many demographies and markers supported).
Future plans for Bio.PopGen include statistics (the meat of the module, actually) and HapMap support, among others.
Need any feature? Just ask. I cannot promise it, but I will try to address user requests in as much as possible
Filed in: Python, bioinformatics, biopython, population genetics
