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Bioinformatics Advance Access originally published online on December 4, 2006
Bioinformatics 2007 23(4):507-508; doi:10.1093/bioinformatics/btl613
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

cBrother: relaxing parental tree assumptions for Bayesian recombination detection

Fang Fang 1, Jing Ding 4, Vladimir N. Minin 5, Marc A. Suchard 5,6 and Karin S. Dorman 1,2,3,*

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

*To whom correspondence should be addressed.


  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 can be freely downloaded 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.

Contact: kdorman{at}iastate.edu

Associate Editor: Martin Bishop

Received on August 17, 2006; revised on November 27, 2006; accepted on November 28, 2006

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