SlidingBayes: exploring recombination using a sliding window approach based on Bayesian phylogenetic inference.
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.
Paraskevis
D
D
Laboratory for Clinical and Epidemiological Virology, Rega Institute for Medical Research, Katholieke Universiteit Leuven, Minderbroedersstraat 10, B-3000 Leuven, Belgium. dparask@cc.uoa.gr
Deforche
K
K
Lemey
P
P
Magiorkinis
G
G
Hatzakis
A
A
Vandamme
A-M
AM
D000465:Algorithms; D001499:Bayes Theorem; D002874:Chromosome Mapping / Q000379:methods; D004279:DNA, Viral / Q000235:genetics*; D015497:HIV-1 / Q000235:genetics; D008957:Models, Genetic; D015233:Models, Statistical; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D004279:DNA, Viral