Figure 4

Ancestral repeats: Substitution parameters for context-dependent model frequencies and a zero-order Markov chain at the root. Substitution parameter estimates (mean and 95% credibility intervals) for each of the twelve entries of the general time-reversible model in each of the sixteen neighbouring base combination using context-dependent model frequencies and a zero-order Markov chain to specify the ancestral root distribution. Note that the log-scale is used for the y-axis.