Table 5.
Parameter estimates and likelihood values for NtCCDs, using the branch-site model.
| Model | Np | Ln L | Estimates of Parameters | LRT p-Value |
Positive Sites (BEB) |
|---|---|---|---|---|---|
| Model A (Branch g) |
41 | −13551.77 |
p0 = 0.90022, p1 = 0.06108, p2a = 0.03624, p2b = 0.00246, ω0 = 0.08803, ω1 = 1.00000, ω2a = 999.00000, ω2b = 999.00000 |
0.03 | None |
| Model A Null (Branch g) |
40 | −13554.00 |
p0 = 0.86534, p1 = 0.05982, p2a = 0.07000, p2b =0.00484, ω0 = 0.08808, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 |
Not Allowed | |
| Model A (Branch i) |
41 | −13545.47 |
p0 = 0.81697, p1 = 0.05118, p2a = 0.12408, p2b = 0.00777, ω0 = 0.08849, ω1 = 1.00000, ω2a = 11.81766, ω2b = 11.81766 |
0.01 | 131K *, 339I **, 343A *, 349G *, 406F *, 413Y *, 533F * |
| Model A Null (Branch i) |
40 | −13548.71 |
p0 = 0.79861, p1 = 0.05219, p2a = 0.14005, p2b = 0.00915, ω0 = 0.0867, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 |
Not Allowed | |
| Model A (Branch k) |
41 | −13545.83 |
p0 = 0.79074, p1 = 0.04952, p2a = 0.15032, p2b = 0.00941, ω0 = 0.08852, ω1 = 1.00000, ω2a = 999.00000, ω2b = 999.00000 |
0.0009 | None |
| Model A Null (Branch g) |
40 | −13551.29 |
p0 = 0.77180, p1 = 0.05151, p2a = 0.16563, p2b = 0.01105, ω0 = 0.08705, ω1 = 1.00000, ω2a = 1.00000, ω2b = 1.00000 |
Not Allowed |
* p < 0.05, ** p < 0.01. BEB: Bayes empirical Bayes.