PopGen module contains modules to handle
population genetics data, applications and algorithms.
Most of the existing
Bio.PopGen features are of non-core population
genetics functionality. This was seen as feature (and not as a bug) in
order to start building a module with functionality where newbie crass
errors would not have dramatic consequences. Currently, with the
experience accumulated is is possible and desirable to concentrate on
core population genetics functionality (i.e., statistics).
Also worth noticing is that we wrap existing functionality whenever possible. For instance we don’t provide our own coalescent simulator, but we provide wrappers to an existing one which is established and widely used (SIMCOAL2).
The fundamental goal is to have support for “classic” population genetics operations (statistics). This should be provided in an extensible, easy to use and future-proof framework. Code exists (see below on how to find it), but will probably be refactored. Below there is also a with list where you can add your desired features.
Your contributions are most welcome. You should follow the general development guidelines for Biopython.