Forward-time population genetic simulation in Python


Keywords
genetics, genomics, population-genetics, simulation, tree-sequences
License
GPL-3.0
Install
pip install fwdpy11==0.17.0

Documentation

fwdpy11

This is the README for fwdpy11, which is a Python package for forward-time population genetic simulation. It uses fwdpp as its C++ back-end.

Build status

Main:

https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main

Development:

https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev

Conda status

Miscellaneous

Python code style:

Features

  • Pickle-able population objects
  • Parallel computation via multiprocessing or concurrent.futures.
  • Custom temporal samplers to analyze populations during a simulation may be written in pure Python.
  • Flexible interface for simulating models with multiple populations.

Documentation

The manual can be found here.

License

GPLv3 or later (See COPYING)

Supported Python version

fwdpy11 is written for Python 3. We will not modify the package to be compatible with Python 2.7.

Dependencies and installation

These topics are covered in the user manual:

Citation

If you use this software for research, please cite the following publications:

  • Kevin R Thornton. Polygenic adaptation to an environmental shift: temporal dynamics of variation under gaussian stabilizing selection and additive effects on a single trait. Genetics, 213(4):1513–1530, December 2019.
  • Kevin R Thornton. A c++ template library for efficient forward-time population genetic simulation of large populations. Genetics, 198(1):157–166, September 2014.

This software was developed for the first paper. The second paper describes a key part of this software's back end.