TABLE 1.
The marginal likelihoods for some of the models examined in this studya
| Model | A | B | C | D | E | F |
| JC69 | – 1345 | – 2319 | – 460 | – 1981 | – 1553 | – 1779 |
| F81 | – 1328 | – 2320 | – 435 | – 1959 | – 1497 | – 1737 |
| HKY85 | – 1279 | – 2233 | – 432 | – 1820 | – 1469 | – 1733 |
| GTR | – 1266 | – 2231 | – 437 | – 1822 | – 1463 | – 1726 |
| JC69 + Γ | – 1308 | – 2211 | – 460 | – 1968 | – 1530 | – 1768 |
| F81 + Γ | – 1286 | – 2213 | – 435 | – 1946 | – 1465 | – 1720 |
| HKY85 + Γ | – 1225 | – 2118 | – 433 | – 1797 | – 1421 | – 1714 |
| GTR + Γ | – 1223 | – 2120 | – 438 | – 1799 | – 1421 | – 1716 |
| NCM-JC69 | – 1345 | – 2398 | – 471 | – 2024 | – 1563 | – 1804 |
| NCM-GTR | – 1266 | – 2314 | – 449 | – 1869 | – 1477 | – 1752 |
| NCM-GTRC | – 1353 | – 2419 | – 473 | – 2035 | – 1572 | – 1811 |
a
The columns give the results for the sequence alignments of (A) gophers, (B) fish of the family Labridae, (C) seed plants of the family Ericales, (D) primates, (E) vertebrate ATPase8 gene, and (F) vertebrate ND4L gene. The three variants of the no common mechanism model are: NCM-JC69, the parameterization discussed by Tuffley and Steel (1997); NCM-GTR, the no common mechanism model implemented with the GTR model with the parameters of the GTR model shared across sites and branches; and NCM-GTRC, the no common mechanism model with independently estimated GTR parameters for each site and branch.