Table 3 Human, mouse, chicken and frog 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 | -7722 | -7728 | -7731 |
| Â | mouse | -7708 | -7728 | -7731 |
Albumin | chicken | -7723 | -7731 | -7731 |
| Â | frog | -7705 | -7728 | -7731 |
| Â | interior | -7723 | -7728 | -7731 |
| Â | human | -2608 | -2619 | -2620 |
| Â | mouse | -2607 | -2619 | -2620 |
ATP6 | chicken | -2590 | -2619 | -2620 |
| Â | frog | -2585 | -2618 | -2620 |
| Â | interior | -2585 | -2618 | -2620 |
| Â | human | -679 | -680 | -682 |
| Â | mouse | -677 | -681 | -682 |
ATP8 | chicken | -675 | -679 | -682 |
| Â | frog | -678 | -680 | -682 |
| Â | interior | -675 | -680 | -682 |
| Â | human | -3872 | -3885 | -3887 |
| Â | mouse | -3869 | -3885 | -3887 |
Cmyc | chicken | -3854 | -3883 | -3887 |
| Â | frog | -3814 | -3882 | -3887 |
| Â | interior | -3853 | -3883 | -3887 |
| Â | human | -4704 | -4792 | -4794 |
| Â | mouse | -4709 | -4791 | -4794 |
COX1 | chicken | -4700 | -4794 | -4794 |
| Â | frog | -4679 | -4791 | -4794 |
| Â | interior | -4698 | -4792 | -4794 |
| Â | human | -2382 | -2399 | -2400 |
| Â | mouse | -2382 | -2399 | -2400 |
COX2 | chicken | -2377 | -2398 | -2400 |
| Â | frog | -2375 | -2398 | -2400 |
| Â | interior | -2376 | -2399 | -2400 |
| Â | human | -2502 | -2537 | -2542 |
| Â | mouse | -2503 | -2540 | -2542 |
COX3 | chicken | -2483 | -2538 | -2542 |
| Â | frog | -2485 | -2539 | -2542 |
| Â | interior | -2486 | -2540 | -2542 |
| Â | human | -3782 | -3833 | -3836 |
| Â | mouse | -3783 | -3832 | -3836 |
CYTB | chicken | -3760 | -3832 | -3836 |
| Â | frog | -3747 | -3832 | -3836 |
| Â | interior | -3760 | -3833 | -3836 |
| Â | human | -3457 | -3483 | -3486 |
| Â | mouse | -3443 | -3483 | -3486 |
ND1 | chicken | -3435 | -3484 | -3486 |
| Â | frog | -3434 | -3482 | -3486 |
| Â | interior | -3442 | -3482 | -3486 |
| Â | human | -4275 | -4298 | -4300 |
| Â | mouse | -4275 | -4298 | -4300 |
ND2 | chicken | -4258 | -4298 | -4300 |
| Â | frog | -4253 | -4296 | -4300 |
| Â | interior | -4255 | -4299 | -4300 |
| Â | human | -1348 | -1353 | -1355 |
| Â | mouse | -1347 | -1351 | -1355 |
ND3 | chicken | -1337 | -1353 | -1355 |
| Â | frog | -1335 | -1352 | -1355 |
| Â | interior | -1335 | -1353 | -1355 |
| Â | human | -5382 | -5406 | -5406 |
| Â | mouse | -5380 | -5406 | -5406 |
ND4 | chicken | -5366 | -5404 | -5406 |
| Â | frog | -5345 | -5405 | -5406 |
| Â | interior | -5365 | -5405 | -5406 |
| Â | human | -1259 | -1261 | -1265 |
| Â | mouse | -1259 | -1264 | -1265 |
ND4L | chicken | -1254 | -1262 | -1265 |
| Â | frog | -1245 | -1263 | -1265 |
| Â | interior | -1254 | -1263 | -1265 |
| Â | human | -7053 | -7089 | -7094 |
| Â | mouse | -7053 | -7091 | -7094 |
ND5 | chicken | -7034 | -7093 | -7094 |
| Â | frog | -7006 | -7090 | -7094 |
| Â | interior | -7029 | -7091 | -7094 |
| Â | human | -2022 | -2025 | -2028 |
| Â | mouse | -2020 | -2025 | -2028 |
ND6 | chicken | -1995 | -2023 | -2028 |
| Â | frog | -1998 | -2025 | -2028 |
| Â | interior | -1998 | -2025 | -2028 |