Branch transducer (conditionally-normalized Pair SCFG) of the TKF Structure Tree model.

The state types for this model are shown in Table 3. The branch transducer evolves a sequence and structure along a branch of the phylogenetic tree. States and are the states for a sub-model corresponding to an insertion of a new stem in the descendant sequences; the sub-model (not shown) is identical in structure to the singlet transducer shown in Table 2. and are the equilibrium distributions of, respectively, descendant unpaired nucleotide and descendant paired nucleotides ; and are the conditional distributions (i.e., match probabilities) of a descendant unpaired nucleotide given an ancestral unpaired nucleotide and descendant paired nucleotides given ancestral nucleotides . The functions , and are parametrized by the insertion and deletion rates of the TKFST model and are defined in “A simple model of RNA structural evolution”.