Table 3.
Results of PAML branch-site model analysis of 256 taxa tree with fitness changes with a magnitude specified by S
| d | S | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 0.1 | 0.5 | 1 | 5 | 10 | 0 | 0.1 | 0.5 | 1 | 5 | 10 | |
| θ = 0.01 | θ = 0.05 | |||||||||||
| 0.01 | – | – | – | – | – | – | – | – | – | – | – | – |
| 0.1 | – | – | – | * | – | – | – | – | – | – | – | – |
| 0.2 | – | – | – | – | – | – | – | – | – | – | – | – |
| 0.5 | * | * | * | * | * | * | * | * | * | * | * | – |
| 1.0 | * | * | * | * | * | * | * | * | * | * | * | * |
| d | S | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 0 | 0.1 | 0.5 | 1 | 5 | 10 | 0 | 0.1 | 0.5 | 1 | 5 | 10 | |
| θ = 0.1 | θ = 0.2 | |||||||||||
| 0.01 | – | – | – | – | – | – | – | – | – | – | – | – |
| 0.1 | – | – | – | – | – | – | – | – | – | |||
| 0.2 | – | – | * | – | – | – | – | * | * | – | – | |
| 0.5 | * | – | – | * | – | – | * | * | – | – | – | – |
| 1.0 | * | * | * | * | * | – | * | * | – | – | – | – |
( indicates absence of positive selection). Data sets where PAML could not detect the presence of positive selection with the LRT are shown by a “–”. * represents data sets where the LRT indicated the presence of positive selection, but no sites undergoing positive selection were identified. indicates data sets where the LRT indicated positive selection, and the BEB correctly identified some of the sites