[Biopython-dev] Bio.PopGen status

Tiago Antão tiagoantao at gmail.com
Thu Aug 30 14:20:32 UTC 2007


This is a small mail to inform all of the effort to create a Bio.PopGen.

What is currently available doesn't still deserve to be called a
Population Genetics module per se. But I think we are getting there...
So what is available?

There is code, test code and documentation for working with GenePop
files, a format which I suppose is reasonably widely used in
population genetics (at least when not considering sequence based
data). I am thinking in closing the related bug.

There is code, test code and documentation (in this case, under
review) to work with Fdist. FDist is a moderately used selection
detection application. The main purpose of this code is to serve as a
"commit exercise" of moderate dimension before starting to commit more
important stuff (therefore learning and making mistakes with a less
important component).

3 important parts follow: Statistics, Coalescent Simulations and
HapMap. For these parts there is already code written...

Statistics: Ralph Haygood sent me code to deal with sequence based
data. I have myself code to deal with no-sequence based data. I will
work on merging both code bases. Documentation and test code will
follow. At this point I think we could say that we have a bare bones
Bio.PopGen module.

Coalescent Simulations: There exists written (and published on a
journal) code to work with simcoal2. Most documentation is also
written. At this point I would guess Bio.PopGen would compare rather
favorably with BioPerl.

HapMap: Part of the code is written, but more will have to be done.

This is the current status of things as I see it from here...
Comments, corrections, discussion would be most welcome...


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