Ffpopsim

FFPopSim is a collection of C++ classes and a Python interface for efficient simulation of large populations, in particular when the product of mutation rate and population size is larger than one. It consists of one library for individual-based simulations, and a complementary one for simulation of the entire genotype distribution. The latter is coded efficiently using Fast-Fourier Transforms to speed up recombination operations.

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Install / Use

/learn @neherlab/Ffpopsim

About this skill

Quality Score

0/100

README

License: GPL3
Author: Richard Neher, Fabio Zanini
Creation: 2012/09/12

Description

Genetic drift and draft

FFPopSim is a C++ and Python library to simulate large populations that are polymorphic at many loci. It allows for asexual and recombining populations and complex fitness functions, including pairwise and higher order epistasis. It is designed to study the effects of linked selection, the rare processes in large populations, and can be used to address a large variety of population genetics problems.

FFPopSim is easy to use via the Python interface and can be extended or modified both at the C++ or Python level.

Downloads

The official sources and releases are online at:

https://github.com/neherlab/ffpopsim

https://github.com/iosonofabio/ffpopsim

Docs

Documentation and examples are online at:

http://webdav.tuebingen.mpg.de/ffpopsim/

http://ffpopsim.readthedocs.io/en/latest/

(The latter only for the Python interface.)

Install

To install using pip:

pip install FFPopSim

To install the library, read the INSTALL file. The two configuration files are:

Makefile
setup.py (for the Python extension)

Enjoy.

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