Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences

By Mark J. Gibbs, J. Armstrong, A. Gibbs. Bioinform., 2000

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Molecular Evolution of Zika Virus during Its Emergence in the 20th Century (2014, background): “4.8 program [31] that incorporates RDP [32], GENECONV [33], Chimaera [34], MaxChi [35], Bootscan [36], SiScan [37] and 3Seq [38] methods to uncover evidence for recombination events.”
RDP4: Detection and analysis of recombination patterns in virus genomes (2015, methodology): “Besides the original RDP method (Martin and Rybicki 2000), these methods include BOOTSCAN (Salminen et al. 1995), MAXCHI (Maynard Smith 1992), CHIMAERA (Posada and Crandall 2001), 3 SEQ (Boni, Posada, and Feldman 2007), GENECONV (Padidam, Sawyer, and Fauquet 1999), LARD (Holmes, Worobey, and Rambaut”
An Exact Nonparametric Method for Inferring Mosaic Structure in Sequence Triplets (2007, methodology): “The most common among these triplet tests—the Chimaera method (Posada and Crandall 2001; Posada 2002), which is based on a x2-statistic (Maynard Smith 1992), and the Martin– Rybicki (MR) binomial distribution test (Martin and Rybicki 2000)—identify unusually high levels of sequence similarity inside”