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Table 1 Human, chimpanzee and gorilla Log-likelihoods (rounded to closest integer) of the MLEs for three 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 -1320 -1324 -1324
ATP6 chimp -1318 -1323 -1324
  gorilla -1318 -1322 -1324
  human -384 -389 -392
ATP8 chimp -384 -389 -392
  gorilla -384 -389 -392
  human -2842 -2876 -2877
COX1 chimp -2846 -2874 -2876
  gorilla -2834 -2875 -2876
  human -1285 -1293 -1295
COX2 chimp -1286 -1294 -1295
  gorilla -1281 -1292 -1295
  human -1477 -1493 -1496
COX3 chimp -1476 -1493 -1496
  gorilla -1472 -1493 -1496
  human -2205 -2236 -2236
CYTB chimp -2208 -2235 -2236
  gorilla -2203 -2235 -2236
  human -1787 -1804 -1805
ND1 chimp -1783 -1804 -1805
  gorilla -1776 -1802 -1805
  human -1949 -1974 -1975
ND2 chimp -1950 -1974 -1975
  gorilla -1941 -1974 -1975
  human -663 -679 -680
ND3 chimp -666 -679 -680
  gorilla -665 -679 -680
  human -2593 -2612 -2613
ND4 chimp -2589 -2612 -2613
  gorilla -2579 -2612 -2613
  human -519 -525 -525.8
ND4L chimp -523 -525 -525.8
  gorilla -520 -526 -525.8
  human -3600 -3624 -3629
ND5 chimp -3611 -3628 -3629
  gorilla -3583 -3628 -3629
  human -913 -917 -918
ND6 chimp -912 -917 -918
  gorilla -913 -917 -918