[BioPython] PopGen module for Biopython?

[Ralph Haygood]

Fellow Biopythoneers,

I'm a population geneticist (currently working at Duke University).
Since last spring, I've written a Python module for computing a
variety of population-genetic statistics from DNA sequences, including
popular favorites such as Tajima's D, Fu and Li's D, and Fay and Wu's
H.  It can compute statistics for a whole alignment, or it can slide a
window along an alignment, or it can compare a pair of congruent
alignments (e.g., transcription factor binding sites versus other
sites in a cis-regulatory region).  It runs under Biopython, in that
it works on Bio.Align.Generic.Alignment objects.

I've used this module extensively (it has contributed to two
manuscripts currently making their ways toward publication).  Where
possible, I've compared its output with that of DnaSP, a widely used
Windows application for population-genetic analyses (however, I wrote
the module mostly to do things that can't be done with DnaSP or any
other canned program I know of).  So I'm confident it's largely
correct.  Now I'm wondering whether there would be interest in adding
it to Biopython.  Bioperl has a module for population-genetic analyses
(written by my colleague Jason Stajich).  I think it would be nice for
Biopython to have one too.

Before my code could be added, I would need to spend a little time on
stylistic modifications and more on documentation.  I'm willing to
spend the time if there would be interest.  There are no intellectual
property obstructions.  Distribution of my code under the Biopython
License Agreement would be fine.

Ralph Haygood