This is the homepage for fwdpy, which is an Python package for forward-time population- and quantitative- genetic simulations.
The source code is here
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.
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
These examples use Python's built-in multiprocessing features to run simulations and synchronize writing output from multiple threads:
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:
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