https://github.com/molpopgen/fwdpy11
Forward-time simulation in Python using fwdpp
https://github.com/molpopgen/fwdpy11
genetics genomics population-genetics simulation tree-sequences
Last synced: 5 months ago
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Forward-time simulation in Python using fwdpp
- Host: GitHub
- URL: https://github.com/molpopgen/fwdpy11
- Owner: molpopgen
- License: gpl-3.0
- Created: 2017-03-20T17:01:57.000Z (almost 9 years ago)
- Default Branch: main
- Last Pushed: 2025-08-13T15:40:38.000Z (6 months ago)
- Last Synced: 2025-08-13T17:39:26.278Z (6 months ago)
- Topics: genetics, genomics, population-genetics, simulation, tree-sequences
- Language: C++
- Homepage: https://molpopgen.github.io/fwdpy11
- Size: 32.2 MB
- Stars: 31
- Watchers: 4
- Forks: 6
- Open Issues: 11
-
Metadata Files:
- Readme: README.rst
- License: COPYING
Awesome Lists containing this project
README
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:
.. image:: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main
:target: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=main
.. image:: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main
:target: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=main
Development:
.. image:: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev
:target: https://github.com/molpopgen/fwdpy11/workflows/Tests/badge.svg?branch=dev
.. image:: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev
:target: https://github.com/molpopgen/fwdpy11/workflows/UbuntuStressTest/badge.svg?branch=dev
Conda status
-----------------------
.. image:: https://anaconda.org/bioconda/fwdpy11/badges/version.svg
:target: https://anaconda.org/bioconda/fwdpy11
.. image:: https://anaconda.org/bioconda/fwdpy11/badges/platforms.svg
:target: https://anaconda.org/bioconda/fwdpy11
Miscellaneous
-----------------------
Python code style:
.. image:: https://img.shields.io/badge/code%20style-black-000000.svg
:target: https://github.com/psf/black
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:
* People wishing to run `fwpdy11` should see `this section `_.
* Those who need to build the package from source should look `the developer's guide `_.
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.
.. _fwdpy11: https://github.com/molpopgen/fwdpy11
.. _fwdpp: https://github.com/molpopgen/fwdpp
.. _GSL: http://gnu.org/software/gsl
.. _pybind11: https://github.com/pybind/pybind11
.. _multiprocessing: https://docs.python.org/3/library/multiprocessing.html
.. _concurrent.futures: https://docs.python.org/3/library/concurrent.futures.html
.. _bioconda: https://bioconda.github.io/
.. _release: https://github.com/molpopgen/fwdpy11/releases
.. _cmake: https://cmake.org