Evaluation of methods for detecting recombination from DNA sequences: empirical data.

By David Posada. Molecular biology and evolution, 2002

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Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects (2003, methodology): “…of recombination detection methods (e.g. Stephens 1985; Hudson & Kaplan 1988; Maynard Smith 1992; Hein 1993; Templeton & Sing 1993; Innan et al. 1996; Maynard Smith & Smith 1998; Wiuf & Hein 1999; McGuire et al. 2000; Schierup & Hein 2000; Xu 2000; Strimmer et al. 2001; reviewed in Posada 2002).”
Automated phylogenetic detection of recombination using a genetic algorithm. (2006, methodology): “We reanalyze two collections of previously published biological sequence align-3 ments (Posada, 2002; Chare, Gould and Holmes, 2003) and compare our ﬁndings to those presented originally.”
RDP2: recombination detection and analysis from sequence alignments (2005, methodology): “A single recombinant sequence in an alignment can seriously influence the branching order and branch lengths of the phylogenetic trees constructed using the alignment (Posada and Crandall, 2002).”
A Simple and Robust Statistical Test for Detecting the Presence of Recombination (2006, methodology): “The Max x(2)-statistic has been found to be the best general test for detecting recombination in a recent empirical study (Posada 2002), and the NSS statistic has been found to be very efficient as well (Brown et al.”