Table 1.
Parameter | M0 | M3 | M1a | M2a | M7 | M8 |
---|---|---|---|---|---|---|
-L | 6185.85 | 6095.77 | 6114.53661 | 6097.91 | 6119.18 | 6098.87 |
2(L1 − L0) | 180.16 (comparison between M0 and M3) | 33.25322 (comparison between M1a and M2a) | 40.62 (comparison between M7 and M8) | |||
chi-square test | p < 0.001 | p < 0.001 | p < 0.001 | |||
d.f. (between 2 models) | 4 | 2 | 2 | |||
Parameter estimates | ω = 0.10026 | ω0 = 0.02378, p0 = 0.76904; ω1 = 0.34981, p1 = 0.22444; ω2 = 1.84622, p2 = 0.00652 | Not allow | ω0 = 0.02948, p0 = 0.80713; ω1 = 1, p1 = 0.01564; ω2 = 0.4, p2 = 0.17724 | ω0 = 0, p0 = 0.5; ω1 = 0.24135, p1 = 0.5 | ω0 = 0, p0 = 0.47944; ω1 = 0.15589, p1 = 0.47944; ω2 = 1, p2 = 0.04111 |
Positive selected sites | Not allow | 64 Q, pa = 0.997; 123 V, pa = 0.995 | Not allow | 64 Q, pb = 0.846; 123 V, pb = 0.808 | Not allow | 64 Q, pb = 0.981; 123 V, pb = 0.972; 223 M, pb = 0.635; 350 G, pb = 0.572; 360 P, pb = 0.532 |
a: probability in naive empirical bayes (NEB) analysis; b: probability in bayes empirical bayes (BEB) analysis; d.f: degree of freedom; ω: dN/dS ratio; p: proportion; L: log likelihood; M0: one ratio model; M1a: nearly neutral model; M2a: positive selection model; M3: discrete model; M7: beta model; M8: beta and ω model.