Perfect Storm

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

I would like to make a preemptive defensive comment on the new population genetics module.

I am, for now, the sole author of the code that is there (although, in future versions there will be at least code from another person. By the way, if YOU want to participate, your 100% welcome). Although the code is mine there was a lot of help from Peter Cock, one of Biopython’s core developers. Without him, this initial groundwork would not have been possible.

Now for the preemptive defense :

If you look at the module, it has very little functionality included. This is a very deliberate strategy to start small and grow slowly. I am expecting for some feedback (which will be very little, I am sure). I want to grow in small steps, including as much feedback as possible. Test code and documentation have to exist before releasing anything to the public.

In the pipeline there is code for coalescent simulation, statistics (including code supplied by Ralph Haygood, that I am joining with my own) and HapMap. If you are interested in early access to any of this code, please give me a shout as most of it already exists. Alpha testers are more than welcome .