Table 2 Human, chimpanzee, gorilla and orangutan Log-likelihoods (rounded to closest integer) of the MLEs for five rooted trees under the nonstationary (NONSTA), stationary (STA) and reversible (REV) models. If NONSTA or STA places the root correctly, the corresponding log likelihood appears in bold.
From: Rooting a phylogenetic tree with nonreversible substitution models
gene | root placement | NONSTA | STA | REV |
|---|---|---|---|---|
| Â | human | -1649 | -1654 | -1655 |
| Â | chimp | -1647 | -1654 | -1655 |
ATP6 | gorilla | -1647 | -1654 | -1655 |
| Â | orangutan | -1642 | -1654 | -1655 |
| Â | interior | -1647 | -1654 | -1655 |
| Â | human | -510 | -514 | -517 |
| Â | chimp | -510 | -515 | -517 |
ATP8 | gorilla | -509 | -515 | -517 |
| Â | orangutan | -509 | -515 | -517 |
| Â | interior | -509 | -515 | -517 |
| Â | human | -3456 | -3465 | -3467 |
| Â | chimp | -3450 | -3464 | -3467 |
COX1 | gorilla | -3448 | -3465 | -3467 |
| Â | orangutan | -3437 | -3465 | -3467 |
| Â | interior | -3453 | -3465 | -3467 |
| Â | human | -1485 | -1496 | -1497 |
| Â | chimp | -1485 | -1496 | -1497 |
COX2 | gorilla | -1481 | -1492 | -1497 |
| Â | orangutan | -1479 | -1492 | -1497 |
| Â | interior | -1480 | -1492 | -1497 |
| Â | human | -1769 | -1791 | -1796 |
| Â | chimp | -1780 | -1791 | -1796 |
COX3 | gorilla | -1781 | -1794 | -1796 |
| Â | orangutan | -1772 | -1794 | -1796 |
| Â | interior | -1780 | -1791 | -1796 |
| Â | human | -2593 | -2673 | -2674 |
| Â | chimp | -2594 | -2673 | -2674 |
CYTB | gorilla | -2590 | -2672 | -2674 |
| Â | orangutan | -2581 | -2672 | -2674 |
| Â | interior | -2588 | -2672 | -2674 |
| Â | human | -2214 | -2234 | -2236 |
| Â | chimp | -2210 | -2235 | -2236 |
ND1 | gorilla | -2205 | -2234 | -2236 |
| Â | orangutan | -2191 | -2233 | -2236 |
| Â | interior | -2209 | -2235 | -2236 |
| Â | human | -2441 | -2469 | -2470 |
| Â | chimp | -2443 | -2469 | -2470 |
ND2 | gorilla | -2437 | -2469 | -2470 |
| Â | orangutan | -2423 | -2469 | -2470 |
| Â | interior | -2437 | -2469 | -2470 |
| Â | human | -837 | -855 | -856 |
| Â | chimp | -840 | -855 | -856 |
ND3 | gorilla | -838 | -856 | -856 |
| Â | orangutan | -834 | -855 | -856 |
| Â | interior | -838 | -855 | -856 |
| Â | human | -3151 | -3206 | -3209 |
| Â | chimp | -3149 | -3205 | -3209 |
ND4 | gorilla | -3141 | -3205 | -3209 |
| Â | orangutan | -3169 | -3207 | -3209 |
| Â | interior | -3145 | -3206 | -3209 |
| Â | human | -623 | -631 | -631 |
| Â | chimp | -622 | -631 | -631 |
ND4L | gorilla | -620 | -631 | -631 |
| Â | orangutan | -619 | -631 | -631 |
| Â | interior | -621 | -631 | -631 |
| Â | human | -4469 | -4501 | -4503 |
| Â | chimp | -4474 | -4502 | -4503 |
ND5 | gorilla | -4453 | -4502 | -4503 |
| Â | orangutan | -4448 | -4503 | -4503 |
| Â | interior | -4466 | -4502 | -4503 |
| Â | human | -1069 | -1076 | -1078 |
| Â | chimp | -1067 | -1076 | -1078 |
ND6 | gorilla | -1070 | -1077 | -1078 |
| Â | orangutan | -1068 | -1077 | -1078 |
| Â | interior | -1069 | -1076 | -1078 |