Probabilistic divergence measures for detecting interspecies recombination.
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.
Husmeier
D
D
Biomathematics & Statistics Scotland, SCRI, Invergowrie, Dundee, DD2 5DA, UK. dirk@bioss.ac.uk
Wright
F
F
D019295:Computational Biology; D004247:DNA / Q000235:genetics; D003716:Dengue Virus / Q000235:genetics; D005821:Genetic Techniques / Q000706:statistics & numerical data; D006515:Hepatitis B virus / Q000235:genetics; D006801:Humans; D008390:Markov Chains; D008957:Models, Genetic; D015233:Models, Statistical; D009010:Monte Carlo Method; D010802:Phylogeny; D011995:Recombination, Genetic; D016415:Sequence Alignment / Q000706:statistics & numerical data; D013045:Species Specificity
D004247:DNA