maxchi(input_file, breaks, winHalfWidth, permReps)chisqs chisqs For a given position of the moving window on the sequence alignment, and for a given pair of sequences, a chi-square statistic is computed to compare two proportions: the proportion of sites at which the sequences agree in the left half-window and the proportion of sites in at which the sequences agree in the right half-window. Discordance between the two proportions may reflect a recombination event, located at the window centre, in the history of the two sequences. The maximum chi-square over all sequence pairs is regarded as a summary of the evidence for recombination at the window centre. The individual chi-square statistics may also be of interest for suggesting pairs of sequences segments that descend from historical recombination events. Significance of observed chi-square 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]
Maynard Smith J (1992). Analyzing the mosaic structure of genes. J Mol Evol, 34:126-129.
summary.maxchi, phylpro