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Bioinformatics Advance Access originally published online on March 13, 2009
Bioinformatics 2009 25(11):1442-1444; doi:10.1093/bioinformatics/btp145
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© The Author 2009. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

SimMLST: simulation of multi-locus sequence typing data under a neutral model

Xavier Didelot 1,*, Daniel Lawson 2 and Daniel Falush 3

1Department of Statistics, University of Warwick, Coventry, 2Department of Mathematics, University of Bristol, Bristol, UK and 3Department of Microbiology, University College Cork, Cork, Ireland

*To whom correspondence should be addressed.


  Abstract

Summary: Multi-locus sequence typing (MLST) is a widely used method of characterization of bacterial isolates. It has been applied to over 50 000 isolates in over 50 different species. Here, we present a coalescent method to jointly simulate MLST data and the clonal genealogy that gave rise to the sample.

Availability and Implementation: SimMLST was implemented in C++and Qt4 for the graphical user interface. It is distributed under the terms of the GNU General Public License. Source code and binaries for Windows and Linux are available from http://go.warwick.ac.uk/SimMLST. A user guide and a technical description of the algorithm are provided with the program.

Contact: X.Didelot{at}warwick.ac.uk

Associate Editor: Martin Bishop

Received on February 17, 2009; revised on March 9, 2009; accepted on March 11, 2009

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