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Figure 1 | BMC Bioinformatics

Figure 1

From: Statistical power of phylo-HMM for evolutionarily conserved element detection

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.

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