Figure 7
From: XRate: a fast prototyping, training and annotation tool for phylo-grammars
An excerpt from an xgram-format grammar reproducing the RNA secondary structure phylo-SCFG of Knudsen and Hein. This excerpt shows only the transformation rules, and omits the alphabet and chain definitions. Two separate Markov chains for nucleotide substitution are used (and are assumed to be defined elsewhere in the file): LNUC and RNUC denote the left and right (i.e. 5' and 3') nucleotides of a co-evolving basepair in a 16-state Markov chain (annotated with characters < and >), while NUC denotes an unpaired nucleotide in a 4-state Markov chain (annotated with character _).