provides an implementation of the "pair
stochastic tree adjoining grammars (PSTAGs)" for
modeling 'pseudoknot' RNA structures, which is an
extension of the "pair hidden
Markov models on tree structures (PHMMTSs)".
PSTAG is a novel method for structural alignment to align and predict
RNA secondary structures including pseudoknots.
By structural alignment, we mean a pairwise alignment
to align "an unfolded RNA sequence" into "an RNA
sequence of known secondary structure".