Table 1.

Parameter estimates and likelihood values under branch and branch-site models.

Model	P	likelihood	Parameters estimated	Positively selected sites
Branch Models
1ω	1	-1431.66	ω all branches = 0.048	N/A
2ω	2	-1431.41	ω placental mammals = 0.054; background = 0.04	N/A
3ω	3	-1408.70	ω anthropoid = 0.431; ω other placentals = 0.008; ω background = 0.042	N/A
Free Ratio	55	-1388.00	ω estimated independently for each branch (see Fig. 1)	N/A
Branch-site models
Model A	4	-1399.23	p0 = 0.90; p1 = 0.012; p(2a+2b) = 0.085; ω0 = 0.021; ω1 = 1; background ω2a = 0.021; ω2b = 1; foreground, ω2a = ω2b = 4.61	5 (1.00); 38 (0.99); 41 (0.53); 64 (1.00); 70 (0.97)
Model A (omega fixed)	3	-1403.73	p0 = 0.80; p1 = 0.011; p(2a+2b) = 0.192; ω0 = 0.02; ω1 = 1; background ω2a = 0.02; ω2b = 1; foreground, ω2a = ω2b = 1	Not allowed

P, number of parameters. Numbers in parentheses represent the posterior probability of each amino acid listed to be in the class of sites under positive selection.