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Bioinformatics Vol. 17 no. 90001 2001
Pages S123-S131
© 2001 Oxford University Press

Probabilistic divergence measures for detecting interspecies recombination

Dirk Husmeier and Frank Wright

Biomathematics & Statistics Scotland, SCRI, Invergowrie, Dundee, DD2 5DA, UK

Received on February 6, 2001 ; revised on April 1, 2001 ; accepted on April 1, 2001

This paper proposes a graphical method for detecting interspecies recombination in multiple alignments of DNA sequences. A fixed-size window is moved along a given DNA sequence alignment. For every position, the marginal posterior probability over tree topologies is determined by means of a Markov chain Monte Carlo simulation. Two probabilistic divergence measures are plotted along the alignment, and are used to identify recombinant regions. The method is compared with established detection methods on a set of synthetic benchmark sequences and two real-world DNA sequence alignments.

Contact: dirk{at}bioss.ac.uk


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