FFPopSim: An efficient forward simulation package for the evolution of large populations

Preprint

30 July 2012

preprint
Published by arXiv in arXiv

https://doi.org/10.48550/arXiv.1207.6916

Abstract

The analysis of the evolutionary dynamics of a population with many polymorphic loci is challenging since a large number of possible genotypes needs to be tracked. In the absence of analytical solutions, forward computer simulations are an important tool in multi-locus population genetics. The run time of standard algorithms to simulate sexual populations increases as 8^L with the number L of loci, or with the square of the population size N. We have developed algorithms that allow to simulate large populations with a run-time that scales as 3^L. The algorithm is based on an analog of the Fast-Fourier Transform (FFT) and allows for arbitrary fitness functions (i.e. any epistasis) and genetic maps. The algorithm is implemented as a collection of C++ classes and a Python interface.

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Version 1, 2012-07-30, ArXiv

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