title: SimBac: simulation of whole bacterial genomes with homologous recombination.
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 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.
authors.affiliation: 1​ Doctoral Training Centre, University of Oxford, Oxford, UK.
authors.forename: Thomas
authors.initials: T
authors.lastname: Brown
authors.affiliation: 2​ Department of Infectious Disease Epidemiology, Imperial College, London, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: 3​ Institute for Emerging Infections, Oxford Martin School, Oxford, UK.|4​ Nuffield Department of Medicine, University of Oxford, Oxford, UK.|5​ Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
authors.forename: Daniel J
authors.initials: DJ
authors.lastname: Wilson
authors.affiliation: 4​ Nuffield Department of Medicine, University of Oxford, Oxford, UK.|3​ Institute for Emerging Infections, Oxford Martin School, Oxford, UK.
authors.forename: Nicola De
authors.initials: N
authors.lastname: Maio
mesh_terms: D001419:Bacteria / Q000145:classification / Q000235:genetics; D003198:Computer Simulation; D016680:Genome, Bacterial / Q000235:genetics*; D059765:Homologous Recombination; D010802:Phylogeny; D012984:Software / Q000592:standards
keywords: bacterial evolution; bacterial genomics; bacterial recombination; coalescent simulation