Work

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

Year: 2004

Type: article

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

Source: Bioinformatics

DOI: 10.1093/bioinformatics/bti139

Authors: D. Paraskevis, K. Deforche, P. Lemey, G. Magiorkinis, A. Hatzakis, A.-M. Vandamme

Institutions: Rega Institute for Medical Research, KU Leuven, National and Kapodistrian University of Athens

Language: English

Topic: Genomics and Phylogenetic Studies

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

Open Access status: bronze

Funders: European Commission, Fonds Wetenschappelijk Onderzoek

Awards: G4896066933, G7885626610