Figure 1.
Two-state phylo-HMM. (A) State-transition diagram: The system consists of a state for conserved sites (c) and a state for nonconserved sites (n). The two states are associated with different phylogenetic models (ψc and ψn). The state-transition probabilities are defined by two parameters (μ and ν) as illustrated. (B) An illustrative alignment generated by this model: A state sequence (Z) is generated according to μ and ν. For each site in the state sequence, a nucleotide is generated for the root node in the phylogenetic tree and then for subsequent child node according to the phylogenetic model (ψc or ψn). The observed alignment (X) is composed of all nucleotides in the leaf nodes. The segment of adjacent conserved sites (in the gray box) is called a conserved element.