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Bioinformatics Advance Access published online on December 4, 2006
Bioinformatics, doi:10.1093/bioinformatics/btl613
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© 2006 The Author(s)
Received August 17, 2006
Revised November 27, 2006
Accepted November 28, 2006

Applications note

cBrother: relaxing parental tree assumptions for Bayesian recombination detection

Fang Fang 1, Jing Ding 2, Vladimir N. Minin 3, Marc A. Suchard 4, and Karin S. Dorman 5 *

1 Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
2 Ohio State University Medical Center, Columbus, OH, 43220, USA
3 Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
4 Department of Biomathematics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA; Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
5 Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA; Department of Statistics, Iowa State University, Ames, IA 50011, USA; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA 50011, USA

* To whom correspondence should be addressed.
Karin S. Dorman, E-mail: kdorman{at}iastate.edu


  Abstract

Summary: Bayesian multiple change-point models accurately detect recombination in molecular sequence data. Previous Java-based implementations assume a fixed topology for the representative parental data. cBrother is a novel C language implementation that capitalizes on reduced computational time to relax the fixed tree assumption. We show that cBrother is 19 times faster than its predecessor and the fixed tree assumption can influence estimates of recombination in a medically-relevant dataset.

Availability: cBrother is freely downloadable from http://www.biomath.org/dormanks/ and can be compiled on Linux, Macintosh, and Windows operating systems. Online documentation and a tutorial are also available at the site.

Associate Editor: Martin Bishop
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