Table 2. Lists of methods and algorithms of the four recombination analysis tools.

Program	Method	Implemented algorithms	Publication Year
SimPlot	Phylogenetic methods, Pairwise sequence comparisons	Similarity/distance plot, Bootscanning	1999
RIP	Pairwise sequence comparisons	Similarity/distance plot	1995
jpHMM		Jumping profile hidden Markov models, Hidden Markov models	2009
RDP3	Phylogenetic methods, Patterns of sites, Pairwise sequence comparisons	Sawyer's statistical test for gene conversion, Maximum chi-squared, Similarity/distance plot, Bootscanning, Difference in Sums of Squares method, Graphical recombination detection using Phylogenetic Profiles, Likelihood Analysis of Recombination in DNA, Sister scanning method, RDP method, Automated bootscanning (Recscan), Recombination detection using multiple approaches, Recombination detection using hyper-geometric random walks.	2010