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Efficient ancestry and mutation simulation with msprime 1.0
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(2022) Efficient ancestry and mutation simulation with msprime 1.0. Genetics, 220 (3). iyab229. doi:10.1093/genetics/iyab229 ISSN 0016-6731.
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Official URL: https://doi.org/10.1093/genetics/iyab229
Abstract
Stochastic simulation is a key tool in population genetics, since the models involved are often analytically intractable and simulation is usually the only way of obtaining ground-truth data to evaluate inferences. Because of this, a large number of specialized simulation programs have been developed, each filling a particular niche, but with largely overlapping functionality and a substantial duplication of effort. Here, we introduce msprime version 1.0, which efficiently implements ancestry and mutation simulations based on the succinct tree sequence data structure and the tskit library. We summarize msprime’s many features, and show that its performance is excellent, often many times faster and more memory efficient than specialized alternatives. These high-performance features have been thoroughly tested and validated, and built using a collaborative, open source development model, which reduces duplication of effort and promotes software quality via community engagement.
Item Type: | Journal Article | |||||||||||||||||||||||||||||||||||||||||||||
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Subjects: | Q Science > QA Mathematics | |||||||||||||||||||||||||||||||||||||||||||||
Divisions: | Faculty of Science, Engineering and Medicine > Science > Statistics | |||||||||||||||||||||||||||||||||||||||||||||
Library of Congress Subject Headings (LCSH): | Stochastic processes -- Mathematical models, Population genetics -- Mathematical models, Mutations (Algebra) | |||||||||||||||||||||||||||||||||||||||||||||
Journal or Publication Title: | Genetics | |||||||||||||||||||||||||||||||||||||||||||||
Publisher: | Genetics Society of America | |||||||||||||||||||||||||||||||||||||||||||||
ISSN: | 0016-6731 | |||||||||||||||||||||||||||||||||||||||||||||
Official Date: | March 2022 | |||||||||||||||||||||||||||||||||||||||||||||
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Volume: | 220 | |||||||||||||||||||||||||||||||||||||||||||||
Number: | 3 | |||||||||||||||||||||||||||||||||||||||||||||
Article Number: | iyab229 | |||||||||||||||||||||||||||||||||||||||||||||
DOI: | 10.1093/genetics/iyab229 | |||||||||||||||||||||||||||||||||||||||||||||
Status: | Peer Reviewed | |||||||||||||||||||||||||||||||||||||||||||||
Publication Status: | Published | |||||||||||||||||||||||||||||||||||||||||||||
Access rights to Published version: | Restricted or Subscription Access | |||||||||||||||||||||||||||||||||||||||||||||
Date of first compliant deposit: | 13 December 2021 | |||||||||||||||||||||||||||||||||||||||||||||
Date of first compliant Open Access: | 24 March 2022 | |||||||||||||||||||||||||||||||||||||||||||||
Funder: | Bjarki Eldon: DFG grant 273887127 through priority programme SPP1819 (STE325/17-2) and Icelandic Research Fund Grant of Excellence 185151-051. Franz Baumdicker: DFG EXC 2064/1 - project 390727645 and DFG EXC 2124 - project 390838134. Gertjan Bisschop and | |||||||||||||||||||||||||||||||||||||||||||||
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