Table 4.
Positive Selection Predictions for the Vertebrate Data Set.
| No Rate Variation versus Codon Gamma Rate Variation | |||||
|---|---|---|---|---|---|
| Significance Threshold of 0.05 | FDR Threshold of 0.1 | ||||
| A | Codon variation | B | Codon variation | ||
| No variation | − | + | No variation | − | + |
| − | 7,063 | 58 | − | 7,660 | 6 |
| + | 823 | 963 | + | 966 | 275 |
|
| |||||
| No Rate Variation versus Codon 3-Rate Variation | |||||
| Significance Threshold of 0.05 | FDR Threshold of 0.1 | ||||
|
| |||||
| C | Codon variation | D | Codon variation | ||
| No variation | − | + | No variation | − | + |
| − | 7,059 | 62 | − | 7,660 | 6 |
| + | 777 | 1,009 | + | 951 | 290 |
|
| |||||
| No Rate Variation versus Site Rate Variation | |||||
| Significance Threshold of 0.05 | FDR Threshold of 0.1 | ||||
|
| |||||
| E | Site variation | F | Site variation | ||
| No variation | − | + | No variation | − | + |
| − | 7,069 | 52 | − | 7,657 | 9 |
| + | 516 | 1,270 | + | 694 | 547 |
|
| |||||
| Site Rate Variation versus Codon Gamma Rate Variation | |||||
| Significance Threshold of 0.05 | FDR Threshold of 0.1 | ||||
|
| |||||
| G | Codon variation | H | Codon variation | ||
| Site variation | − | + | Site variation | − | + |
| − | 7,513 | 72 | − | 8,347 | 4 |
| + | 373 | 949 | + | 279 | 277 |
note.—Numbers in each cell indicate how many branches were detected (+) or not detected (−) to be evolving under positive selection by different variants of the branch-site model.