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Bioinformatics Advance Access originally published online on May 24, 2005
Bioinformatics 2005 21(13):3034-3042; 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{at}oupjournals.org

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

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

1Department of Biomathematics, David Geffen School of Medicine, University of California Los Angeles, CA 90095-1766, USA
2Department of Statistics, Iowa State University Ames, IA 50011, USA
3Department of Genetics, Cell & Development Biology, Iowa State University Ames, IA 50011, USA
4Bioinformatics and Computational Biology Program, Iowa State University Ames, IA 50011, USA

*To whom correspondence should be addressed.

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 previously by Suchard and co-workers. 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 Markov chain Monte Carlo 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

Contact: msuchard{at}ucla.edu

Supplementary information: http://www.biomath.ucla.edu/msuchard/DualBrothers


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