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

• DOI: 10.1093/bioinformatics/bts633
• Publication Date: 2012-10-25T00:56:29Z
• Authors: Fabio Zanini; Richard A. Neher
• Keywords: Python; Epistasis

The analysis of the evolutionary dynamics a population with many polymorphic loci is challenging, as large number possible genotypes needs to be tracked. In absence analytical solutions, forward computer simulations are an important tool in multi-locus genetics. run time standard algorithms simulate sexual populations increases 8(L) L, or square size N.We have developed arbitrary genetic maps, including multiple crossovers, that scales 3(L). If crossovers restricted at most one, reduced L2(L). algorithm based on analogue Fast Fourier Transform (FFT) and allows for fitness functions (i.e. any epistasis). addition, we include streamlined individual-based framework. library implemented collection C++ classes Python interface.