Table 5.
Parameter estimates and likelihood ratio tests for the branch-site models
| Model | p a | LnLb | Estimates of Parameters | 2△lc | df | p | Positively selected sites |
|---|---|---|---|---|---|---|---|
| M1: Neutral (k=2) | 1 | -47271.650 | p 0=0.774, (p 1=0.226) | ||||
| Branch-site models | |||||||
| Model A (I-1) | 3 | -47231.883 | p 0 = 0.416, p 1 = 0.123, (p 2a+p 2b=0.461), ω2 =1.291 | Model A vs M1: 79.535 | 2 | 0.000 | Site for foreground lineage: 15 (at p>0.95) |
| Model A (II-1) | 3 | -47271.650 | p 0=0.774, p 1= 0.226, (p 2a+p 2b =0.000), ω2=2.639 | Model A vs M1: 0.000 | 2 | 1.000 | |
| Model A (II-2) | 3 | -47271.650 | p 0 = 0.774, p 1 = 0.226, (p 2a+p 2b=0.000), ω2 =1.000 | Model A vs M1: 0.000 | 2 | 1.000 | |
| Model A (II-3) | 3 | -47253.663 | p 0=0.740, p 1= 0.214, (p 2a+p 2b =0.046), ω2=28.900 | Model A vs M1: 35.974 | 2 | 0.000 | Site for foreground lineage: 1 (at p>0.95) |
| Model A (II-4) | 3 | -47264.889 | p0=0.707, p1= 0.207, (p 2a+p 2b =0.085), ω2=1.506 | Model A vs M1: 13.523 | 2 | 0.001 | |
| Model A (II-5) | 3 | -47257.978 | p 0=0.718,p 1= 0.210, (p 2a+p 2b =0.072), ω2=3.022 | Model A vs M1: 27.345 | 2 | 0.000 | |
aThe number of free parameters for the ω ratios
bLikelihood of the model
c2(l1-l0)