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Bioinformatics Advance Access originally published online on April 21, 2006
Bioinformatics 2006 22(18):2317-2318; doi:10.1093/bioinformatics/btl153
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

GeneRecon—a coalescent based tool for fine-scale association mapping

Thomas Mailund 1,2,4,*, Mikkel H. Schierup 1,2, Christian N. S. Pedersen 1,2,3, Jesper N. Madsen 2, Jotun Hein 4 and Leif Schauser 1,2

1 Bioinformatics Research Center, University of Aarhus Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark
2 Bioinformatics ApS Høegh-Guldbergs Gade 10, DK-8000 Århus C, Denmark
3 Department of Computer Science, University of Aarhus IT-Parken, DK-8200 Århus N, Denmark
4 Department of Statistics, University of Oxford Oxford, OX1 3TG, UK

*To whom correspondence should be addressed.

Summary: GeneRecon is a tool for fine-scale association mapping using a coalescence model. GeneRecon takes as input case–control data from phased or unphased SNP and microsatellite genotypes. The posterior distribution of disease locus position is obtained by Metropolis-Hastings sampling in the state space of genealogies. Input format, search strategy and the sampled statistics can be configured through the Guile Scheme programming language embedded in GeneRecon, making GeneRecon highly configurable.

Availability: The source code for GeneRecon, written in C++ and Scheme, is available under the GNU General Public License (GPL) at http://www.birc.au.dk/~mailund/GeneRecon

Contact: mailund{at}birc.au.dk

Received on February 8, 2006; revised on April 5, 2006; accepted on April 16, 2006

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