Singlet transducer (single-sequence SCFG) of the TKF Structure Tree model.

The state types for this model are shown in Table 1. The singlet transducer generates ancestral RNA sequences and structures. We use the notation of formal grammars to represent state transformation rules; for example, the rule corresponds to (in a Pair HMM) an state emitting a nucleotide and then making a self-transition. Both loop ( and ) and stem ( and ) sequence evolve as TKF sequences with length parameters and (defined in “A simple model of RNA structural evolution”). and are the equilibrium distributions of unpaired nucleotides and paired nucleotides and are normalized such that and . The bifurcation state is used to end stem sequences (only loop sequences are allowed to transition to the empty string).