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Molecular Biology and Evolution, Vol 15, 326-335, Copyright © 1998 by Society for Molecular Biology and Evolution

ORIGINAL ARTICLE

Phylogenetic profiles: a graphical method for detecting genetic recombinations in homologous sequences

GF Weiller
Bioinformatics Laboratory, Research School of Biological Sciences, Australian National University, Canberra, ACT, Australia. weiller@rsbs.anu.edu.au

Phylogenetic profiles constitute a novel way of graphically displaying the coherence of the sequence relationships over the entire length of a set of aligned homologous sequences. Using a sliding-window technique, this method determines the pairwise distances of all sequences in the windows and evaluates, for each sequence, the degree to which the patterns of distances in these regions agree. This method is suited for exploring data consistency as well as detecting recombinant sequences. A computer program implementing the algorithm has been developed, and examples with simulated and natural sequences are given to demonstrate the sensitivity and accuracy of the method for identifying recombinant sequences and their recombination junctions as well as detecting hot spots of recombinational activity.
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