phylpro(input_file, breaks, winHalfWidth, permReps)corrscorrsFor a given position of the moving window on the sequence alignment, and for a given “target” sequence, a correlation is computed to compare two distance vectors: the distance between the target sequence and all other sequences in the left half-window and the distance between the target sequence and all others in the right half-window. The pair-wise distance measure used is the proportion of sites at which the sequences differ. Discordance between the two distance vectors may reflect a recombination event, located at the window centre, in the history of the target sequence. The minimum correlation over all target sequences is regarded as a summary of the evidence for recombination at the window centre. The individual correlations for the target sequences may also be of interest for suggesting sequence segments that descend from historical recombination events. Significance of observed correlation statistics is assessed by a Monte Carlo permutation test. When conditioning on breakpoints proposed at previous steps of a stepwise search, permutation is restricted to sites within blocks defined by the previously proposed breakpoints, as described by Graham et al. (2004).
Graham J, McNeney B and Seillier-Moiseiwitsch F (2004). Stepwise detection of recombination breakpoints in sequence alignments. Bioinformatics Sep 23; [Epub ahead of print]
Weiller G (1998). Phylogenetic profiles: A graphical method for detecting genetic recombination in homologous sequences. Mol Biol Evol, 15:326-335.
summary.phylpro, maxchi