Table 3.
Positively selected sites, log-likelihood scores and parameter estimates for the Rickettsia ompB gene
| Model | Parameters in the ω distribution | l | Positively selected codons |
|---|---|---|---|
| M0, one ratio | ω = 0.48 | −19,832.06 | None |
| M3, discrete | ω1 = 0.09, p1 = 0.60 ω2 = 1.01, p2 = 0.36 ω3 = 4.89, (p3 = 0.04) | −19,315.01 | 53V, 60P, 122H, 205V, 487V, 538G, 591A, 639D, 720V, 742I, 789A, 804F, 820G, 856G, 906T, 912S, 959I, 988A, 1075F, 1139R |
| M7, beta | p = 0.19, q = 0.26 | −19,418.60 | Not allowed |
| M8, beta+ω | p = 0.26, q = 0.39, p1 = 0.94 ω = 4.20, (p2 = 0.06) | −19,316.34 | 53V, 60P, 122H, 205V, 466A, 487V, 507G, 538G, 591A, 639D, 720V, 742I, 762A, 789A, 804F, 820G, 856G, 906T, 912S, 959I, 988A, 1075F, 1139R, 1594V |
| M8A, beta+ω = 1 | p = 1.31 q = 11.70, p1 = 0.64 (ω = 1, p2 = 0.36) | −19,399.97 | Not allowed |
Details in legend of Table 2