Table 1.

Summary of the four models analyzed

Substitution Model	Marginal Likelihood	50% credible set size	Mean tree height (years)
(a) GTR + CP + strict	-3656.13 ± 0.11	38	70.1 ± 0.09
(b) GTR + CP + relaxed	-3655.33 ± 0.11	57	70.5 ± 0.2
(c) GTR + Γ + I + strict	-3751.37 ± 0.11	289	71.7 ± 0.1
(d) GTR + Γ + I + relaxed	-3750.23 ± 0.11	469	72.0 ± 0.2

The marginal likelihoods, the number of distinct tree topologies in the 50% credible set and the mean tree height (± stderr) of the four substitution models that were analyzed in the example. The large improvement in marginal likelihood clearly indicates that the two codon-position substitution models (CP) are substantially superior to the models in which rate heterogeneity among sites is modeled by a 3-distribution and a proportion of invariant sites. In contrast, in this example there is little difference in fit to the data between the strict clock and the relaxed clock analyses, suggesting that this data is clock-like.