Bacmeta : simulator for genomic evolution in bacterial metapopulations

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dc.contributor University of Helsinki, Department of Mathematics and Statistics en
dc.contributor University of Helsinki, Jukka Corander / Principal Investigator en
dc.contributor.author Sipola, Aleksi
dc.contributor.author Marttinen, Pekka
dc.contributor.author Corander, Jukka
dc.date.accessioned 2019-06-29T21:47:40Z
dc.date.available 2021-06-16T02:47:22Z
dc.date.issued 2018-07-01
dc.identifier.citation Sipola , A , Marttinen , P & Corander , J 2018 , ' Bacmeta : simulator for genomic evolution in bacterial metapopulations ' , Bioinformatics , vol. 34 , no. 13 , pp. 2308-2310 . https://doi.org/10.1093/bioinformatics/bty093 en
dc.identifier.issn 1367-4803
dc.identifier.other PURE: 114862861
dc.identifier.other PURE UUID: 2f4ffec2-de23-4399-b952-bd6f2f4d8ba2
dc.identifier.other WOS: 000438247800090
dc.identifier.other Scopus: 85050793000
dc.identifier.uri http://hdl.handle.net/10138/303631
dc.description.abstract The advent of genomic data from densely sampled bacterial populations has created a need for flexible simulators by which models and hypotheses can be efficiently investigated in the light of empirical observations. Bacmeta provides fast stochastic simulation of neutral evolution within a large collection of interconnected bacterial populations with completely adjustable connectivity network. Stochastic events of mutations, recombinations, insertions/deletions, migrations and micro-epidemics can be simulated in discrete non-overlapping generations with a Wright-Fisher model that operates on explicit sequence data of any desired genome length. Each model component, including locus, bacterial strain, population and ultimately the whole metapopulation, is efficiently simulated using C++ objects and detailed metadata from each level can be acquired. The software can be executed in a cluster environment using simple textual input files, enabling, e.g. large-scale simulations and likelihood-free inference. Availability and implementation: Bacmeta is implemented with C++ for Linux, Mac and Windows. It is available at https://bitbucket.org/aleksisipola/bacmeta under the BSD 3-clause license. Contact: aleksi.sipola@helsinki.fi or jukka.corander@medisin.uio.no Supplementary information: Supplementary data are available at Bioinformatics online. en
dc.format.extent 3
dc.language.iso eng
dc.relation.ispartof Bioinformatics
dc.rights en
dc.subject APPROXIMATE BAYESIAN COMPUTATION en
dc.subject POPULATION-GENETICS en
dc.subject RECOMBINATION en
dc.subject COALESCENT en
dc.subject MODELS en
dc.subject 1183 Plant biology, microbiology, virology en
dc.subject 112 Statistics and probability en
dc.title Bacmeta : simulator for genomic evolution in bacterial metapopulations en
dc.type Article
dc.description.version Peer reviewed
dc.identifier.doi https://doi.org/10.1093/bioinformatics/bty093
dc.type.uri info:eu-repo/semantics/other
dc.type.uri info:eu-repo/semantics/acceptedVersion
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