Recombination and phylogeny: effects and detection
International Journal of Bioinformatics Research and Applications
RB-Finder: an improved distance-based sliding window method to detect recombination breakpoints
RECOMB'07 Proceedings of the 11th annual international conference on Research in computational molecular biology
Reassortment Networks for Investigating the Evolution of Segmented Viruses
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Motivation: A promising sliding-window method for the detection of interspecific recombination in DNA sequence alignments is based on the monitoring of changes in the posterior distribution of tree topologies with a probabilistic divergence measure. However, as the number of taxa in the alignment increases or the sliding-window size decreases, the posterior distribution becomes increasingly diffuse. This diffusion blurs the probabilistic divergence signal and adversely affects the detection accuracy. The present study investigates how this shortcoming can be redeemed with a pruning method based on post-processing clustering, using the Robinson--Foulds distance as a metric in tree topology space. Results: An application of the proposed scheme to three synthetic and two real-world DNA sequence alignments illustrates the amount of improvement that can be obtained with the pruning method. The study also includes a comparison with two established recombination detection methods: Recpars and the DSS (difference of sum of squares) method. Availability: Software, data and further supplementary material are available at the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/ Contact: dirk@bioss.ac.uk