Table 5.

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

Branch-site model
Foreground branches	Estimates of parameter				Positive delection sites(BEB)
	Site class 0	Site class 1	Site class 2a	Site class 2b
	P0 = 0.10272	P1 = 0.36090	P2a = 0.11884	P2b = 0.41754
Group 1	ω0(b) = 0.05880	ω1(b) = 1.00000	ω2a(b) = 0.05880	ω2b(b) = 1.00000	None
	ω0(f) = 0.05880	ω1(f) = 1.00000	ω2a(f) = 1.00000	ω2b(f) = 1.00000
	P0 = 0.45646	P1 = 0.17985	P2a = 0.26089	P2b = 0.10279
Group 2a	ω0(b) = 0.05165	ω1(b) = 1.00000	ω2a(b) = 0.05165	ω2b(b) = 1.00000	None
	ω0(f) = 0.05165	ω1(f) = 1.00000	ω2a(f) = 1.00000	ω2b(f) = 1.00000
	P0 = 0.42991	P1 = 0.34434	P2a = 0.12535	P2b = 0.10040
Group 2b	ω0(b) = 0.11089	ω1(b) = 1.00000	ω2a(b) = 0.11089	ω2b(b) = 1.00000	359 G*
	ω0(f) = 0.11089	ω1(f) = 1.00000	ω2a(f) = 999.00000	ω2b(f) = 999.00000
	P0 = 0.20480	P1 = 0.56991	P2a = 0.05956	P2b = 0.16573	171 K**, 181 Q**,
Group 2c	ω0(b) = 0.06509	ω1(b) = 1.00000	ω2a(b) = 0.06509	ω2b(b) = 1.00000	192S**, 210 A**,
	ω0(f) = 0.06509	ω1(f) = 1.00000	ω2a(f) = 5.55679	ω2b(f) = 5.55679	237 S**, 243 I**
	P0 = 0.55167	P1 = 0.13832	P2a = 0.24786	P2b = 0.06215	25 N**, 26 I**, 34 C**, 79 S**,
Group 2d	ω0(b) = 0.08684	ω1(b) = 1.00000	ω2a(b) = 0.08684	ω2b(b) = 1.00000	148 T**, 208 G**, 214 D**,
	ω0(f) = 0.08684	ω1(f) = 1.00000	ω2a(f) = 214.85997	ω2b(f) = 214.85997	269 H**, 363 C**, 395 N**
	P0 = 0.27330	P1 = 0.60581	P2a = 0.03758	P2b = 0.08331
Group 2e	ω0(b) = 0.08686	ω1(b) = 1.00000	ω2a(b) = 0.08686	ω2b(b) = 1.00000	196 E*
	ω0(f) = 0.08686	ω1(f) = 1.00000	ω2a(f) = 44.60691	ω2b(f) = 44.60691
	P0 = 0.42970	P1 = 0.32076	P2a = 0.14288	P2b = 0.10666
Group 3	ω0(b) = 0.07702	ω1(b) = 1.00000	ω2a(b) = 0.07702	ω2b(b) = 1.00000	107 F*
	ω0(f) = 0.07702	ω1(f) = 1.00000	ω2a(f) = 999.00000	ω2b(f) = 999.00000

Note: *p < 0.05 and **p < 0.01 (x² test).

Site class: The sites in the sequence evolve according to the same process, the transition probability matrix is calculated only once for all sites for each branch.

b: Background ω.

f: Foreground ω.

Positive delection sites: The number of amino acid sites estimated to have undergone positive selection.

BEB: Bayes Empirical Bayes.