Table 5.

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

Foreground branches	Estimates of parameter				positive selection sites (BEB) 4
	Site class 1 0	Site class 1	Site class 2a	Site class 2b
Group I	P0 = 0.50799	P1 = 0.05716	P2a = 0.39087	P2b = 0.04398	296Q*,337A*,397 K*,407D*,
	ω0(b)2 = 0.13998	ω1(b) = 1.00000	ω2a(b) = 0.13998	ω2b(b) = 1.00000	412 L*,415P**,419H*,446 T*,
	ω0(f)3 = 0.13998	ω1(f) = 1.00000	ω2a(f) = 3.03087	ω2b(f) = 3.03087	453 F**,457 L*,464C*,476E**, 505 T**,510Q*,527A*, 535 V*
Group II	P0 = 0.63235	P1 = 0.07147	P2a = 0.26611	P2b = 0.03007	644 L*
	ω0(b) = 0.13987	ω1(b) = 1.00000	ω2a(b) = 0.13987	ω2b(b) = 1.00000
	ω0(f) = 0.13987	ω1(f) = 1.00000	ω2a(f) = 1.16777	ω2b(f) = 1.16777
Group III	P0 = 0.69273	P1 = 0.07803	P2a = 0.20604	P2b = 0.02321	None
	ω0(b) = 0.14005	ω1(b) = 1.00000	ω2a(b) = 0.14005	ω2b(b) = 1.00000
	ω0(f) = 0.14005	ω1(f) = 1.00000	ω2a(f) = 999.00000	ω2b(f) = 999.00000
Group IV	P0 = 0.86848	P1 = 0.04356	P2a = 0.08376	P2b = 0.00420	328Q*, 368S**
	ω0(b) = 0.13026	ω1(b) = 1.00000	ω2a(b) = 0.13026	ω2b(b) = 1.00000
	ω0(f) = 0.13026	ω1(f) = 1.00000	ω2a(f) = 20.88429	ω2b(f) = 20.88429
Group V	P0 = 0.63670	P1 = 0.03187	P2a = 0.31563	P2b = 0.01580	296Q**,303A**,412 L**,418 F*, 453 F*,490 W**,497D**,508 L**, 511R**, 513A**, 518 T**,
	ω0(b) = 0.12995	ω1(b) = 1.00000	ω2a(b) = 0.12995	ω2b(b) = 1.00000
	ω0(f) = 0.12995	ω1(f) = 1.00000	ω2a(f) = 1.56269	ω2b(f) = 1.56269
Group VI	P0 = 0.72413	P1 = 0.03621	P2a = 0.22825	P2b = 0.01141	448 K*, 456 K**, 515 K**
	ω0(b) = 0.12948	ω1(b) = 1.00000	ω2a(b) = 0.12948	ω2b(b) = 1.00000
	ω0(f) = 0.12948	ω1(f) = 1.00000	ω2a(f) = 1.26601	ω2b(f) = 1.26601
Group VII	P0 = 0.71371	P1 = 0.03569	P2a = 0.23866	P2b = 0.01194	297C**, 335S*, 497D*, 551R*
	ω0(b) = 0.12951	ω1(b) = 1.00000	ω2a(b) = 0.12951	ω2b(b) = 1.00000
	ω0(f) = 0.12951	ω1(f) = 1.00000	ω2a(f) = 76.78801	ω2b(f) = 76.78801

Note: *p < 0.05 and **p < 0.01 (x ² test).

¹The sites in the sequence evolve according to the same process, the transition probability matrix is calculated only once for all sites for each branch.

²Background ω.

³Foreground ω.

⁴The number of amino acid sites estimated to have undergone positive selection; BEB: Bayes Empirical Bayes.