Figure 2.

Ancestral repeats: Influence of root sequence distributions on model fit (against independence throughout the entire tree) using context-dependent model frequencies. Various orders of Markov chains for the ancestral root sequence are tested against the assumption of site-independent evolution throughout the entire tree using the context-dependent model with context-dependent model frequencies, revealing once again that a second-order Markov chain yields the largest increase in model fit vis-à-vis the independent GTR model. Both annealing and melting schemes are shown for each model comparison. The 95% confidence intervals are at most 30 log units wide (not shown).