Figure 3

A complete covariance model. Right: the CM corresponding to the alignment in Figure 1. The model has 81 states (boxes, stacked in a vertical array). Each state is associated with one of the 24 nodes of the guide tree (text to the right of the state array). States corresponding to the consensus are in white. States responsible for insertions and deletions are gray. The transitions from bifurcation state B10 to start states S11 and S46 are in bold because they are special: they are an obligate (probability 1) bifurcation. All other transitions (thin arrows) are associated with transition probabilities. Emission probability distributions are not represented in the figure. Left: the states are also arranged according to the guide tree. A blow up of part of the model corresponding to nodes 6, 7, and 8 shows more clearly the logic of the connectivity of transition probabilities (see main text), and also shows why any parse tree must transit through one and only one state in each "split set".