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

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 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. © The Author 2004. Published by Oxford University Press. All rights reserved.