Illustrating PhyloNet-HMM.

The structure of the HMM (only states are shown) that PhyloNet-HMM builds for the simple scenario of one individual sampled per species in Fig. 2. The three states correspond to genomic regions whose evolution follows the parental tree , and there is a state for each of the three possible local genealogies. The three states correspond to genomic regions whose evolution follows the parental tree , and there is a state for each of the three possible local genealogies. is the start state. See text for emission and transition probabilities.