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Table 3 Results for the large ENCODE data set. Splids \(\ge\) 2 bp were coded and trees were calculated with RAxML using the Gamma model for binary data and ascertainment bias correction
| Mafft G-INS-i | T-Coffee | TBA/Multiz | |
|---|---|---|---|
| Number of sites | 36,132,992 | 36,450,667 | 37,689,662 |
| Number of splids | 545,790 | 922,277 | 919,908 |
| \(d_{RF}\) | 16 | 16 | 12 |
| \(d'_{RF}\) | 0.2424 | 0.2424 | 0.1818 |
| \(d_{Q}\) | 5000 | 7494 | 3710 |
| \(d'_{Q}\) | 0.0849 | 0.1272 | 0.0630 |
