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Bioinformatics Advance Access published online on November 30, 2004
Bioinformatics, doi:10.1093/bioinformatics/bti151
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 10, 2004
Revised November 2, 2004
Accepted November 11, 2004

Article

Detecting interspecific recombination with a pruned probabilistic divergence measure

Dirk Husmeier 1* and Frank Wright 1

1 Biomathematics and Statistics Scotland, JCMB, The King's Buildings, Edinburgh, EH9 3JZ, United Kingdom; Biomathematics and Statistics Scotland, SCRI, Invergowrie, Dundee, DD2 5DA, United Kingdom

* To whom correspondence should be addressed.
Dirk Husmeier, E-mail: dirk{at}bioss.ac.uk


  Abstract

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 postprocessing 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 method.

Availability: Software, data and further supplementary material are available from the following website: http://www.bioss.sari.ac.uk/~dirk/Supplements/.


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