Table 5

Methods for detecting recombination evaluated for performance

MethodImplementationReferenceCategory
1Bootscanning simplot 33, 44Phylogenetic
2Geneconv geneconv 37Substitution
3Homoplasy Test homoplasy test * 42Substitution
4Informative Sites Test pist 43Substitution
5Maximum χ2 maxchi * 41Substitution
6Maximum mismatch χ2 chimaera * D.P., unpublished workSubstitution
7Phylogenetic Profiles phypro * 27Distance
8Partial Likelihood plato 30Phylogenetic
9Rdp rdp 32Phylogenetic
10Recombination Parsimony recpars 28Phylogenetic
11Reticulate reticulate 34Compatibility
12Runs Test runs test * 40Substitution
13Sneath Test sneath test * 38Substitution
14Triple triple * 48Phylogenetic
  • * Local program written in c