Figure 5.

Explicit graphical model representation of a GTR model with a fixed tree topology. For pure convenience, we show here rooted trees that demonstrate the similarity to previous figures. The model of character evolution is a continuous time Markov model parameterized by an instantaneous rate matrix. The rate matrix Q is a deterministic variable computed by multiplying the base frequencies π with the exchangeability rates ε. A Dirichlet distribution is applied as the prior distribution on both the base frequencies π and the exchangeability rates ε. a) A GTR model with fixed branch lengths. b) A GTR model with estimated branch lengths. Each branch length is independent and identically distributed under an exponential distribution.