Skip to main content

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
  human -1649 -1654 -1655
  chimp -1647 -1654 -1655
ATP6 gorilla -1647 -1654 -1655
  orangutan -1642 -1654 -1655
  interior -1647 -1654 -1655
  human -510 -514 -517
  chimp -510 -515 -517
ATP8 gorilla -509 -515 -517
  orangutan -509 -515 -517
  interior -509 -515 -517
  human -3456 -3465 -3467
  chimp -3450 -3464 -3467
COX1 gorilla -3448 -3465 -3467
  orangutan -3437 -3465 -3467
  interior -3453 -3465 -3467
  human -1485 -1496 -1497
  chimp -1485 -1496 -1497
COX2 gorilla -1481 -1492 -1497
  orangutan -1479 -1492 -1497
  interior -1480 -1492 -1497
  human -1769 -1791 -1796
  chimp -1780 -1791 -1796
COX3 gorilla -1781 -1794 -1796
  orangutan -1772 -1794 -1796
  interior -1780 -1791 -1796
  human -2593 -2673 -2674
  chimp -2594 -2673 -2674
CYTB gorilla -2590 -2672 -2674
  orangutan -2581 -2672 -2674
  interior -2588 -2672 -2674
  human -2214 -2234 -2236
  chimp -2210 -2235 -2236
ND1 gorilla -2205 -2234 -2236
  orangutan -2191 -2233 -2236
  interior -2209 -2235 -2236
  human -2441 -2469 -2470
  chimp -2443 -2469 -2470
ND2 gorilla -2437 -2469 -2470
  orangutan -2423 -2469 -2470
  interior -2437 -2469 -2470
  human -837 -855 -856
  chimp -840 -855 -856
ND3 gorilla -838 -856 -856
  orangutan -834 -855 -856
  interior -838 -855 -856
  human -3151 -3206 -3209
  chimp -3149 -3205 -3209
ND4 gorilla -3141 -3205 -3209
  orangutan -3169 -3207 -3209
  interior -3145 -3206 -3209
  human -623 -631 -631
  chimp -622 -631 -631
ND4L gorilla -620 -631 -631
  orangutan -619 -631 -631
  interior -621 -631 -631
  human -4469 -4501 -4503
  chimp -4474 -4502 -4503
ND5 gorilla -4453 -4502 -4503
  orangutan -4448 -4503 -4503
  interior -4466 -4502 -4503
  human -1069 -1076 -1078
  chimp -1067 -1076 -1078
ND6 gorilla -1070 -1077 -1078
  orangutan -1068 -1077 -1078
  interior -1069 -1076 -1078