EWF: simulating exact paths of the Wright–Fisher diffusion

Abstract Motivation The Wright–Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as selection, mutation and genetic drift. Simulating the paths of the process is challenging due to the...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2023-01, Vol.39 (1)
Main Authors: Sant, Jaromir, Jenkins, Paul A, Koskela, Jere, Spanò, Dario
Format: Article
Language:English
Subjects:
Availability
Bioinformatics
Biological activity
Density
Diffusion
Frequency dependence
Gene Frequency
Genetic Drift
Genetics
Genetics, Population
Models, Genetic
Mutation
Population genetics
Samplers
Selection, Genetic
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Summary:Abstract Motivation The Wright–Fisher diffusion is important in population genetics in modelling the evolution of allele frequencies over time subject to the influence of biological phenomena such as selection, mutation and genetic drift. Simulating the paths of the process is challenging due to the form of the transition density. We present EWF, a robust and efficient sampler which returns exact draws for the diffusion and diffusion bridge processes, accounting for general models of selection including those with frequency dependence. Results Given a configuration of selection, mutation and endpoints, EWF returns draws at the requested sampling times from the law of the corresponding Wright–Fisher process. Output was validated by comparison to approximations of the transition density via the Kolmogorov–Smirnov test and QQ plots. Availability and implementation All softwares are available at https://github.com/JaroSant/EWF. Supplementary information Supplementary data are available at Bioinformatics online.
ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btad017