GSpace: an exact coalescence simulator of recombining genomes under isolation by distance

Abstract Motivation Simulation-based inference can bypass the limitations of statistical methods based on analytical approximations, but software allowing simulation of structured population genetic data without the classical n-coalescent approximations (such as those following from assuming large p...

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Published inBioinformatics (Oxford, England) Vol. 37; no. 20; pp. 3673 - 3675
Main Authors Virgoulay, Thimothée, Rousset, François, Leblois, Raphaël
Format Journal Article
LanguageEnglish
Published England Oxford University Press 25.10.2021
Oxford University Press (OUP)
Subjects
Life Sciences
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Summary:Abstract Motivation Simulation-based inference can bypass the limitations of statistical methods based on analytical approximations, but software allowing simulation of structured population genetic data without the classical n-coalescent approximations (such as those following from assuming large population size) are scarce or slow. Results We present GSpace, a simulator for genomic data, based on a generation-by-generation coalescence algorithm taking into account small population size, recombination and isolation by distance. Availability and implementation Freely available at site web INRAe (http://www1.montpellier.inra.fr/CBGP/software/gspace/download.html).
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ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btab261