TABLE 2.

Comparison of the efficiency and accuracy of UPGMA using site-by-site and gene-by-gene bootstrapping, BURST, and our method on simulated data

	Parameters		UPGMAa		UPGMAb		BURST		Our program
Simulation no.	θ/L (×100)	ρ	Efficiency	Accuracy	Efficiency	Accuracy	Efficiency	Accuracy	Efficiency	Accuracy
1	0.2	0	0.16	0.94	0.19	0.90	0.11	0.83	0.17	0.95
2	1.0	0	0.42	0.91	0.44	0.91	0.20	0.84	0.42	0.94
3	5.0	0	0.57	0.85	0.57	0.82	0.15	0.86	0.75	0.94
4	0.2	1	0.14	1.00	0.14	1.00	0.11	0.84	0.19	0.94
5	1.0	1	0.37	0.86	0.38	0.84	0.19	0.82	0.43	0.95
6	5.0	1	0.65	0.85	0.67	0.87	0.15	0.85	0.73	0.93
7	0.2	5	0.14	0.87	0.15	0.88	0.12	0.86	0.19	0.86
8	1.0	5	0.35	0.79	0.38	0.76	0.18	0.80	0.40	0.86
9	5.0	5	0.57	0.74	0.58	0.77	0.14	0.88	0.70	0.90
10	0.2	10	0.21	0.67	0.17	0.85	0.14	0.80	0.19	0.81
11	1.0	10	0.33	0.66	0.34	0.73	0.18	0.80	0.39	0.84
12	5.0	10	0.70	0.85	0.70	0.87	0.16	0.91	0.71	0.89

^aSite-by-site bootstrapping.

^bGene-by-gene bootstrapping.