Table 5.

Methods for detecting recombination evaluated for performance

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6	Maximum mismatch χ2	chimaera*	D.P., unpublished work	Substitution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

^*Local program written in c.