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Bioinformatics Advance Access published online on November 16, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti139
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received October 6, 2003
Revised February 26, 2004
Accepted April 20, 2004

Applications note

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

D. Paraskevis 1*, K. Deforche 2, P. Lemey 2, G. Magiorkinis 3, A. Hatzakis 3, and A.-M. Vandamme 2

1 Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium; National Retrovirus Reference Center, Department of Hygiene and Epidemiology, Athens University Medical School, Mikras Asias 75, GR-11527, Athens, Greece
2 Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium
3 National 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.
D. Paraskevis, E-mail: Dimitris.Paraskevis{at}uz.kuleuven.ac.be


  Abstract

Summary: We developed a software tool (SlidingBayes) for recombination analysis based on Bayesian phylogenetic inference. SlidingBayes 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 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/.

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


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