Table 2.

Probability of recovering the metazoan phylogenies A and C of Figure 3 by different methods in 100 replicate datasets of 2000 and 5000 sites simulated under the site-heterogeneous (SH2) and branch-site-heterogeneous (BSH) models

	SH2				BSH
	tree A		Tree C		Tree A		Tree C
Method	2K	5K	2K	5K	2K	5K	2K	5K
AA	83	98	72	98	57	81	51	88
DNA-123	84	100	76	100	0	0	0	0
DNA-123-P	92	100	78	100	0	0	0	0
DNA-12	86	98	76	100	66	89	58	87
DNA-12-P	82	98	72	100	65	90	59	94
Codon	63	88	46	91	0	0	0	0

Note: Datasets were simulated assuming trees A and C of Figure 3, using parameter estimates from the empirical dataset.