Population Genetics in Biopython

Biopython makes Population Genetics functionality available in the Bio.PopGen module.

  1. Access to Genepop methods (exact tests for Hardy–Weinberg equilibrium, population differentiation, genotypic disequilibrium, F-statistics, null allele frequencies, allele size-based statistics for microsatellites and much more).
  2. Coalescent simulation via SIMCOAL2 and fastsimcoal2.
  3. Selection detection via fdist2

Documentation on how to access Genepop using Bio.PopGen can be found here.

Documentation for interacting with SIMCOAL2 and fdist2 can be found on the PopGen Chapter in the Tutorial (PDF).

Other software

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

Future developments

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