Pair Hidden Markov Models on Tree Structures
PHMMTS (Pair Hidden Markov Models on Tree Structures) aligns a sequence of unknown secondary structure to a sequence of known secondary structure.
Sakakibara, Y: Pair hidden Markov models on tree structures. Bioinformatics, 2003, 19 Supl 1, i232-240 [pubmed]
Sato, K. and Sakakibara, Y.: RNA secondary structural alignment with conditional random fields. Bioinformatics, 2005, 21 Suppl 2, ii237-ii242 [pubmed]