This page provides an implementation of the "pair hidden Markov models on tree structures (PHMMTSs)", which is an extension of the
"pair hidden Markov models (PHMMs)" defined on alignments of trees.

PHMMTS provides a unifying framework and an automata-theoretic model for alignments of trees, structural alignments and pair stochastic context-free grammars.

By structural alignment, we mean a pairwise alignment to align "an unfolded RNA sequence" into "an RNA sequence of known secondary structure".