Table 2. Singlet transducer (single-sequence SCFG) of the TKF Structure Tree model.
| Source→Destinatioon | probability | Source→Destinatioon | probability |
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1 |
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).