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 (ψ_c and ψ_n). 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 (ψ_c or ψ_n). 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.