Table 1 Parameter estimates under branch, site and branch-site models
Model | p | InL | Estimate of parameters | Models compared | 2ΔL |
|---|---|---|---|---|---|
Branch models | |||||
M0: ω0 = ω1 = ω2 = ωc | 1 | −10227.98 | ω0 = ω1 = ω2 = ωc = 0.130 |  |  |
Mf: ω free | 51 | −10109.65 | ω: 0 ~ 0.941 | Mf vs. M0 | 236.66*** |
M2a: ω0 = ω2 = ωc, ω1 | 2 | −10227.97 | ω0 = ω2 = ωc =0.130, ω1 = 0.150 | M2a vs. M0 | 0.02 |
M2b: ω0 =ω1 = ωc, ω2 | 2 | −10227.89 | ω0 = ω1 = ωc = 0.129, ω2 = 0.190 | M2b vs. M0 | 0.18 |
M2c: ω0 = ω1 = ω2, ωc | 2 | −10210.87 | ω0 = ω1 = ω2 = 0.122, ωc = 0.951 | M2c vs. M0 | 34.22*** |
M3a: ω0 = ωc, ω1, ω2 | 3 | −10227.88 | ω0 = ωc = 0.129, ω1 = 0.149, ω2 = 0.190 | M3a vs. M2a | 0.18 |
M3b: ω0 = ω2, ω1, ωc | 3 | −10210.85 | ω0 = ω2 = 0.122, ω1 = 0.153, ω2 = 0.949 | M3b vs. M2c | 0.04 |
M3c: ω0 = ω1, ω2, ωc | 3 | −10212.06 | ω0 = ω1 = 0.121, ω2 = 1.020, ωc = 0.756 | M3c vs. M2c | −2.38 |
M4a: ω0, ω1, ω2, ωc | 4 | −10210.82 | ω0 = 0.122, ω1 = 0.153, ω2 = 0.148, ωc = 0.942 | M4a vs. M2c | 0.10 |
Site-specific models | |||||
M1: nearly neutral | 1 | −10152.15 | P0 = 0.929, P1 = 0.071 ωO =0.109, ω1 = 1.000 |  |  |
M2: PositiveSelection | 3 | −10152.15 | P0 = 0.929, P1 = 0.071, P2 = 0.000 ω0 = 0.109, ω1 = 1.000, ω2 =30.688 | M2 vs. M1 | 0 |
M3: discrete (k=2) | 5 | −10064.21 | P0 = 0.534, P1 = 0.417, P2 = 0.048 ωO = 0.028, ω1 = 0.223, ω2 = 0.670 | M3 vs. M0 | 327.54*** |
M7: beta | 2 | −10064.80 | P = 0.580 q = 3.405 |  |  |
M8: beta & ω | 4 | −10061.64 | p0 = 0.989, p = 0.646, q = 4.203 (p1 = 0.011) ω = 1.054 | M8 vs. M7 | 6.32* |
Branch-site model | |||||
model A | 3 | −10130.51 | P0 = 0.353, p1 = 0.026, p2 = 0.621, ω2 = 1.442 | MA vs.M1 | 43.28*** |