Table 3.

Parameters estimation and likelihood ratio tests for the branch-site models

Hypothesis	lnL	Site class 0	Site class 1	Site class 2a	Site class 2b	2ΔlnL
Alternative	−9212.750	p0 = 0.36828 ω0(b)1 = 0.17271 ω0(f)2 = 0.17271	p1 = 0.56715	p2a = 0.02542	p2b = 0.03915	35.237**
			ω1(b) = 1	ω2a(b) = 0.17271	ω2b(b) = 1
			ω1(f) = 1	ω2a(f) = 999	ω2b(f) = 999
Null	−9230.368	p0 = 0.31965	p1 = 0.45639	p2a = 0.09225	p2b = 0.13171
		ω0(b=)0.17495	ω1(b) = 1.00000	ω2a(b) = 0.17495	ω2b(b) = 1.00000
		ω0(f) = 0.17495	ω1(f) = 1.00000	ω2a(f) = 1.00000	ω2b(f) = 1.00000

Note: **p < 0.01 (χ² test); 1 Background ω; 2 Foreground ω