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. 2007 Feb 23;3(2):e7. doi: 10.1371/journal.pgen.0030007

Figure 2. Graphical Representation of Coal-HMM.

Figure 2

The coal-HMM divides a multiple alignment into four types of segments corresponding to the four phylogenetic states HC1, HC2, HG, and CG. The probability of making a transition from state HC1 to any of the other states is s, and the probability of a transition from any of the HC2, HG, or CG states to state HC1 is u. Transitions between the HC2, HG, and CG states have probability v. The indicated branch lengths of the phylogenetic trees from state HC1 and state CG are divergence times estimated from Target 1. The branch lengths of the phylogenetic trees corresponding to state HC2 and HG are the same as the branch lengths of state CG.