TABLE 2.

Pairwise comparisons of the phylogenetic trees evaluated in this study^a

Phylogenetic tree type	Phylogenetic tree type
	NJ	MP1	MP2	ARB	RAxML	RAxML pars	MrBayes
NJ		142.1	143.0	310.6	198.0	1024.3	333.9
MP1	0.60		17.5	252.7	155.6	1125.6	248.6
MP2	0.62	0.10		246.0	147.8	1125.5	246.3
ARB	0.71	0.70	0.67		287.8	1266.2	316.0
RAxML	0.67	0.60	0.59	0.75		1167.5	189.9
RAxML pars	0.68	0.57	0.56	0.73	0.59		1320.5
MrBayes	0.71	0.46	0.44	0.73	0.61	0.67

^aShown are pairwise comparisons of the phylogenetic trees evaluated in Fig. 2 using the NDA (boldface type; upper triangle of matrix; results are arbitrary values with greater values indicating greater dissimilarity) and a partition metric (lower triangle of matrix; results are fractions indicating dissimilarity, ranging from 0 to 1). Methods are as follows: NJ, neighbor joining, as implemented in NEIGHBOR; MP1 and MP2, maximum parsimony, as implemented in DNAPARS; ARB, parsimony insertion, as implemented in Arb; RAxML, maximum likelihood, as implemented in RAxML; RAxML pars, RAxML parsimony insertion guide tree; MrBayes, Bayesian tree as implemented in MrBayes. All values along the diagonal are 0 for both methods (because each tree is identical to itself).