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EWF : simulating exact paths of the Wright–Fisher diffusion
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Sant, Jaromir, Jenkins, Paul A., Koskela, Jere and Spanò, Dario (2023) EWF : simulating exact paths of the Wright–Fisher diffusion. Bioinformatics, 39 (1). btad017. doi:10.1093/bioinformatics/btad017 ISSN 1367-4803.
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Official URL: http://dx.doi.org/10.1093/bioinformatics/btad017
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 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:
All software is available at https://github.com/JaroSant/EWF
Supplementary information:
Supplementary information is available at Bioinformatics online.
Item Type: | Journal Article | |||||||||||||||||||||
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Subjects: | Q Science > QH Natural history | |||||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Computer Science Faculty of Science, Engineering and Medicine > Science > Statistics |
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Library of Congress Subject Headings (LCSH): | Mathematical statistics, Population genetics -- Mathematical models | |||||||||||||||||||||
Journal or Publication Title: | Bioinformatics | |||||||||||||||||||||
Publisher: | Oxford University Press | |||||||||||||||||||||
ISSN: | 1367-4803 | |||||||||||||||||||||
Official Date: | January 2023 | |||||||||||||||||||||
Dates: |
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Volume: | 39 | |||||||||||||||||||||
Number: | 1 | |||||||||||||||||||||
Article Number: | btad017 | |||||||||||||||||||||
DOI: | 10.1093/bioinformatics/btad017 | |||||||||||||||||||||
Status: | Peer Reviewed | |||||||||||||||||||||
Publication Status: | Published | |||||||||||||||||||||
Access rights to Published version: | Open Access (Creative Commons) | |||||||||||||||||||||
Date of first compliant deposit: | 13 January 2023 | |||||||||||||||||||||
Date of first compliant Open Access: | 16 January 2023 | |||||||||||||||||||||
RIOXX Funder/Project Grant: |
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