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Bioinformatics Advance Access published online on May 24, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti459
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received August 5, 2004
Revised April 14, 2005
Accepted April 18, 2005

Article

Dual multiple change-point model leads to more accurate recombination detection

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

1 Department of Biomathematics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095-1766, USA
2 Department of Statistics, Cell & Development Biology, Iowa State University, Ames, IA 50011, USA; Department of Genetics, Cell & Development Biology, Iowa State University, Ames, IA 50011, USA; Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA
3 Bioinformatics and Computational Biology Program, Iowa State University, Ames, IA 50011, USA

* To whom correspondence should be addressed.
Marc A. Suchard, E-mail: msuchard{at}ucla.edu


  Abstract

Motivation: We introduce a dual multiple change-point (MCP) model for recombination detection among aligned nucleotide sequences. The dual MCP model is an extension of the model introduced by Suchard et al. (2003b). In the original single MCP model, one change-point process is used to model spatial phylogenetic variation. Here, we show that using two change-point processes, one for spatial variation of tree topologies and the other for spatial variation of substitution process parameters, increases recombination detection accuracy. Statistical analysis is done in a Bayesian framework using reversible jump MCMC sampling to approximate the joint posterior distribution of all model parameters.

Results: We use primate mitochondrial DNA data with simulated recombination break-points at specific locations to compare the two models. We also analyze two real HIV sequences to identify recombination break-points using the dual MCP model.

Availability: A software program "DualBrothers" implementing the dual MCP model is available in the form of a Java package at http://www.biomath.ucla.edu/msuchard/DualBrothers.


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