[BioPython] [PopGen] a random Haplotype Sets generator

[Tiago Antão]

> Really the implementation requires some representation of the genetic map.
> After all if the positions are very close, the two loci should not change
> very frequently. I do not know a nice way to represent this even with
> genetic marker simulation (something I do know about). I have not used
> simcoal as my work has moved from genetic markers. Perhaps you need to see
> how simcoal and similar packages do it.

Just for the record, there is an excellent (in all respects: features,
code quality, documentation, author support) forward time population
genetics simulator in python: simuPOP. It is probably the best forward
time simulator that I know of (probably better than the R-based
"competitor" rmetasim, which doesn't have any provision for
selection).
It might be interesting to study how simuPOP represents a genome.

Tiago