Imperial College London
Alternate

DrXavierDidelot

Faculty of Medicine, School of Public Health

Visiting Professor
 
 
 
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Contact

 

+44 (0)20 7594 3622x.didelot

 
 
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Location

 

G30Medical SchoolSt Mary's Campus

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Summary

 

Publications

Citation

BibTex format

@article{Brown:2016:10.1099/mgen.0.000044,
author = {Brown, T and Didelot, X and Wilson, DJ and De, Maio N},
doi = {10.1099/mgen.0.000044},
journal = {Microbial Genomics},
title = {SimBac: simulation of whole bacterial genomes with homologous recombination.},
url = {http://dx.doi.org/10.1099/mgen.0.000044},
volume = {2},
year = {2016}
}
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RIS format (EndNote, RefMan)

TY  - JOUR
AB  - 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.
AU  - Brown,T
AU  - Didelot,X
AU  - Wilson,DJ
AU  - De,Maio N
DO  - 10.1099/mgen.0.000044
PY  - 2016///
SN  - 2057-5858
TI  - SimBac: simulation of whole bacterial genomes with homologous recombination.
T2  - Microbial Genomics
UR  - http://dx.doi.org/10.1099/mgen.0.000044
UR  - http://hdl.handle.net/10044/1/59181
VL  - 2
ER  -
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