The PNarec method for detection of ancient recombinations through phylogenetic network analysis

Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through phylogenetic network analysis, and detected five ancient recombinations in gibbon ABO blood group genes [Kitano et al., 2009. Mol. Phylogenet. Evol., 51, 465–471]. We present applications of this method, now named as “PNarec”, to various virus sequences as well as HLA genes.

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► A new method for detecting ancient recombinations, PNarec, is explained.
► Phylogenetic network construction is involved in the PNarec method.
► The PNarec method was applied to various viral sequence data and HLA data.
► We provide recursive algorithm for the PNarec method.