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