Pair-HMM for the aligment of two graphs. Pair-HMM for the alignment of two graphs. M is the state emitting aligned node pairs, X and Y emit a node in one sequence and a gap in the other one, and H is a silent transient state. As each graph node is associated with an alignment column, the emission probability of a node or a pair of nodes is equal to the likelihood of the corresponding phylogenetic sub-tree based on the characters of these columns. δ is the gap opening probability, ε is the gap extension probability, and ω is the probability of changing to the terminal state.
Szalkowski BMC Bioinformatics 2012 13:129 doi:10.1186/1471-2105-13-129