PopGen

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Python programmers might want to consider [http://pypop.org PyPop] which includes intra-population frequentist statistics and [http://simupop.sourceforge.net/ simuPOP] for foward-time population genetics.
 
Python programmers might want to consider [http://pypop.org PyPop] which includes intra-population frequentist statistics and [http://simupop.sourceforge.net/ simuPOP] for foward-time population genetics.
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[http://www.daimi.au.dk/~mailund/CoaSim/ CoaSim] (coalescent simulation) also exposes a Python interface.
  
 
== Future developments ==
 
== Future developments ==
  
 
Any notes (or discussion) about possible future developments should be restricted to the [[PopGen_dev|PopGen development]] page.
 
Any notes (or discussion) about possible future developments should be restricted to the [[PopGen_dev|PopGen development]] page.

Revision as of 10:21, 20 March 2009

Population genetics in Biopython

Code pertaining population genetics in Bipython can be found in the PopGen module. Most documentation can be found on the PopGen Chapter in the Tutorial (PDF).

Currently, most code available wraps existing functionality provided by external programs, namely SimCoal2 for coalescent simulation and fdist for Fst based selection detection.

Other software

Python programmers might want to consider PyPop which includes intra-population frequentist statistics and simuPOP for foward-time population genetics.

CoaSim (coalescent simulation) also exposes a Python interface.

Future developments

Any notes (or discussion) about possible future developments should be restricted to the PopGen development page.

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