TABLE 3.
Likelihood values and parameter estimates for BFDV CP
| Model code | na | Likelihoodb | dN/dS ratio | Estimates of parametersc |
|---|---|---|---|---|
| Ignoring recombination | ||||
| M3 (3 categories) | 29 | −3,379.21 | 0.534 | p2 = 0.083, ω2 = 2.91 |
| M7 | 29 | −3,399.08 | 0.365 | p = 0.102, q = 0.177 |
| M8 | 29 | −3,381.51 | 0.549 | p0 = 0.84579, p = 0.23812, q = 0.84027, p1 = 0.154, ω = 2.356 |
| Recombinant regions removed | ||||
| M3 (3 categories) | 28 | −3,383.78 | 0.537 | p2 = 0.057, ω2 = 3.44 |
| M7 | 28 | −3,398.29 | 0.392 | p = 0.09449, q = 0.14654 |
| M8 | 28 | −3,384.28 | 0.558 | p0 = 0.90511, p = 0.15727, q = 0.33863, p1 = 0.09489, ω = 2.85629 |
a
Number of sequences in the data set.
b
Log likelihood of the fitted model.
c
For each model, the proportion of sites in the ith category (i = 0, 1, or 2) is reported (pi), together with the values of dN/dS assigned to each category (ωi). p and q are parameters that determine the shape of the beta distribution of ω values in models M7 and M8.