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Bioinformatics Advance Access originally published online on November 16, 2004
Bioinformatics 2005 21(7):1274-1275; doi:10.1093/bioinformatics/bti139
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© The Author 2004. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference

D. Paraskevis 1,2,*, K. Deforche 1, P. Lemey 1, G. Magiorkinis 2, A. Hatzakis 2 and A.-M. Vandamme 1

1Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven Minderbroedersstraat 10, B-3000 Leuven, Belgium
2National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School Mikras Asias 75, GR-11527, Athens, Greece

*To whom correspondence should be addressed.

Summary: We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. Sliding-Bayes provides a powerful approach for detecting potential recombination, especially between highly divergent sequences and complex HIV-1 recombinants for which simpler methods like neighbor joining (NJ) may be less powerful. SlidingBayes guides Markov Chain Monte Carlo (MCMC) sampling performed by MrBayes in a sliding window across the alignment (Bayesian scanning). The tool can be used for nucleotide and amino acid sequences and combines all the modeling possibilities of MrBayes with the ability to plot the posterior probability support for clustering of various combinations of taxa.

Availability: SlidingBayes is available at http://www.kuleuven.ac.be/rega/cev/Software/

Contact: dparask{at}cc.uoa.gr

Supplementary information: A quick guide and examples for SlidingBayes are available at http://www.kuleuven.ac.be/rega/cev/Software/


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