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SimBac: simulation of whole bacterial genomes with homologous recombination
Bacteria can exchange genetic material, or acquire genes found in the environment. This process, generally known as bacterial recombination, can have a strong impact on the evolution and phenotype of bacteria, for example causing the spread of antibiotic resistance across clades and species, but can...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Microbiology Society
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049688/ https://www.ncbi.nlm.nih.gov/pubmed/27713837 http://dx.doi.org/10.1099/mgen.0.000044 |
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author | Brown, Thomas Didelot, Xavier Wilson, Daniel J. Maio, Nicola De |
author_facet | Brown, Thomas Didelot, Xavier Wilson, Daniel J. Maio, Nicola De |
author_sort | Brown, Thomas |
collection | PubMed |
description | Bacteria can exchange genetic material, or acquire genes found in the environment. This process, generally known as bacterial recombination, can have a strong impact on the evolution and phenotype of bacteria, for example causing the spread of antibiotic resistance across clades and species, but can also disrupt phylogenetic and transmission inferences. With the increasing affordability of whole genome sequencing, the need has emerged for an efficient simulator of bacterial evolution to test and compare methods for phylogenetic and population genetic inference, and for simulation-based estimation. We present SimBac, a whole-genome bacterial evolution simulator that is roughly two orders of magnitude faster than previous software and includes a more general model of bacterial evolution, allowing both within- and between-species homologous recombination. Since methods modelling bacterial recombination generally focus on only one of these two modes of recombination, the possibility to simulate both allows for a general and fair benchmarking. SimBac is available from https://github.com/tbrown91/SimBac and is distributed as open source under the terms of the GNU General Public Licence. |
format | Online Article Text |
id | pubmed-5049688 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Microbiology Society |
record_format | MEDLINE/PubMed |
spelling | pubmed-50496882016-10-04 SimBac: simulation of whole bacterial genomes with homologous recombination Brown, Thomas Didelot, Xavier Wilson, Daniel J. Maio, Nicola De Microb Genom Mini-Review Bacteria can exchange genetic material, or acquire genes found in the environment. This process, generally known as bacterial recombination, can have a strong impact on the evolution and phenotype of bacteria, for example causing the spread of antibiotic resistance across clades and species, but can also disrupt phylogenetic and transmission inferences. With the increasing affordability of whole genome sequencing, the need has emerged for an efficient simulator of bacterial evolution to test and compare methods for phylogenetic and population genetic inference, and for simulation-based estimation. We present SimBac, a whole-genome bacterial evolution simulator that is roughly two orders of magnitude faster than previous software and includes a more general model of bacterial evolution, allowing both within- and between-species homologous recombination. Since methods modelling bacterial recombination generally focus on only one of these two modes of recombination, the possibility to simulate both allows for a general and fair benchmarking. SimBac is available from https://github.com/tbrown91/SimBac and is distributed as open source under the terms of the GNU General Public Licence. Microbiology Society 2016-01-19 /pmc/articles/PMC5049688/ /pubmed/27713837 http://dx.doi.org/10.1099/mgen.0.000044 Text en © 2016 The Authors http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/). |
spellingShingle | Mini-Review Brown, Thomas Didelot, Xavier Wilson, Daniel J. Maio, Nicola De SimBac: simulation of whole bacterial genomes with homologous recombination |
title | SimBac: simulation of whole bacterial genomes with homologous recombination |
title_full | SimBac: simulation of whole bacterial genomes with homologous recombination |
title_fullStr | SimBac: simulation of whole bacterial genomes with homologous recombination |
title_full_unstemmed | SimBac: simulation of whole bacterial genomes with homologous recombination |
title_short | SimBac: simulation of whole bacterial genomes with homologous recombination |
title_sort | simbac: simulation of whole bacterial genomes with homologous recombination |
topic | Mini-Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049688/ https://www.ncbi.nlm.nih.gov/pubmed/27713837 http://dx.doi.org/10.1099/mgen.0.000044 |
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