Table 2.

Comparisons of reconstructed phylogenies to the known topology of the dataset

Tree method	Tree name	Fraction of correct parent/child relations	Fraction of correct clades in tree structure
CSI phylogeny, pruning disabled	CSI_all_1	0.73	0.71
CSI phylogeny, pruning set to 10 bp	CSI_all_2	0.52	0.61
CSI phylogeny, pruning disabled NC_000913 as ref	CSI_all_3	0.52	0.61
NDtree, z-score 1.96	ND_all_1	0.65	0.63
NDtree, z-score 1.96, UPGMA tree method	ND_all_2	0.20	0.08
NDtree pairwise comparison, z-score 1.96	ND_all_3	0.26	0.29
NDtree, z-score 1.64	ND_all_4	0.65	0.63
NDtree, NC_000913 as ref, z-score 1.96	ND_all_5	0.65	0.63
NDtree, NC_012759 as ref, z-score 1.96	ND_all_6	0.65	0.63
NDtree, NC_017641 as ref, z-score 1.96	ND_all_7	0.65	0.63
REALPHY, ref NC_012759 and NC_000913, PhyML	RP_all_1	0.55	0.51
REALPHY, ref NC_012759 and NC_000913, RAxML	RP_all_2	0.33	0.24