2012/01/01 by Fabio Zanini, Zanini, Fabio, Richard A. Neher +1
Biochemistry, Genetics and Molecular Biology · Computer Science · #Evolution and Genetic Dynamics #Evolutionary Algorithms and Applications #FOS: Biological sciences #Genetic Mapping and Diversity in Plants and Animals #Populations and Evolution (q-bio.PE) #q-bio.PE
paper · pdf · doi:10.48550/arxiv.1207.6916
available from: http://code.google.com/p/ffpopsim
openalex publication_date 2012/01/01 · arxiv created 2012/07/30 · arxiv updated 2012/07/31 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 8L 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 3L. 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.