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Bioinformatics Advance Access published online on December 6, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl622
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© The Author (2006). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received September 28, 2006
Revised November 21, 2006
Accepted November 28, 2006

Applications note

msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots

Garrett Hellenthal 1 * and Matthew Stephens 2

1 Department of Statistics, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
2 Department of Statistics, University of Chicago, 5734 S. University Avenue, Eckhart 126, Chicago, IL 60637, USA

* To whom correspondence should be addressed.
Garrett Hellenthal, E-mail: hellenth{at}stats.ox.ac.uk


  Abstract

Summary: We have incorporated both crossover and gene conversion hotspots into an existing coalescent-based program for simulating genetic variation data for a sample of chromosomes from a population (Hudson, 2002).

Availability: The source code for msHOT is available by email from hellenth@stats.ox.ac.uk, along with accompanying instructions.

Associate Editor: Keith A Crandall
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