Forward-time population genetic simulation in Python


Keywords
genetics, genomics, population-genetics, simulation, tree-sequences
License
GPL-3.0
Install
pip install fwdpy11==0.18.1

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

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: