Development Page for the PopGen Module.

Introduction

The PopGen module contains modules to handle population genetics data, applications and algorithms.

History and philosophy

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).

Future Goals

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.

Code and contributing

Your contributions are most welcome. You should follow the general development guidelines for Biopython.

Wish list

• support for a binary format - like HDF5 or this one: snpfile
• support for database: it is frequent to carry analysis on a big scale, so it is not unfrequent to use databases to store data