# 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
1. Note: *p < 0.05 and **p < 0.01 (x2 test).
2. 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.
3. b: Background ω.
4. f: Foreground ω.
5. Positive delection sites: The number of amino acid sites estimated to have undergone positive selection.
6. BEB: Bayes Empirical Bayes.