SimBac: simulation of whole bacterial genomes with homologous recombination.
File(s)
Author(s)
Brown, T
Didelot, X
Wilson, DJ
De Maio, N
Type
Journal Article
Abstract
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 modeling 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 http://github.com/tbrown91/SimBac and is distributed as open source under the terms of the GNU General Public License.
Date Issued
2016-01-19
Date Acceptance
2015-12-11
Citation
Microbial Genomics, 2016, 2 (1)
ISSN
2057-5858
Publisher
Microbiology Society
Journal / Book Title
Microbial Genomics
Volume
2
Issue
1
Copyright Statement
© 2016 The Authors. Published by Microbiology Society. This is an open access article published by the Microbiology Society under the Creative Commons Attribution-NonCommercial License.
License URL
Sponsor
Medical Research Council (MRC)
Biotechnology and Biological Sciences Research Council (BBSRC)
Grant Number
MR/K010174/1B
BB/L023458/1
Subjects
bacterial evolution
bacterial genomics
bacterial recombination
coalescent simulation
Publication Status
Published
Date Publish Online
2016-01-19