The fwdpy home page

This is the homepage for fwdpy, which is an Python package for forward-time population- and quantitative- genetic simulations.

Source code

The source code is here

Documentation

The manual is manually generated by us via a separate project hosted on GitHub. We are attempting to make sure that the manual is current with the latest stable release of fwdpy, but that won’t always be the case.

We are attempting to have it automatically build via readthedocs, but that is proving a challenge.

• Manual in html format.

Examples

Here are some examples generated using Ipython/Jupyter:

• Background selection
• “Views” of populations
• Deep copies of simulated populations
• Trajectories of selected mutations
• Recording from simulations over time
• Distribution of fixation times
• Sliding windows

Advanced examples

These examples use Python’s built-in multiprocessing features to run simulations and synchronize writing output from multiple threads:

• Background selection
• Ages of selected alleles

Extending fwdpy

A major goal of fwdpy is to make it extensible, which can be done via Python, Cython, and/or C++. The Cython option simplifies the use of C++ in writing extensions:

• Extending fwdpy using Cython

Citation

If you use fwdpy for yor research, please cite the following manuscript, which is the basis for this package:

• Thornton, K. R. (2014) A C++ template library for efficient forward-time population genetic simulation of large populations. Genetics 98:157-166 PMID: 24950894, Manuscript, Software