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contains a general 16-state model (RNA16), however this model has free parameters
and is not well suited for phylogenetic inference, especially maximum-likelihood inference.
RNA16A is a simplified 16-state model, it reduces some of the complexity of the RNA16
model by cutting down on the number of rate parameters from 120 to 5. It uses a rate
of single transitions , a rate of double transversions , a
non-mismatch transition rate for transitions
requiring only one substitution and a mismatch
rate for transitions requiring one substitution too. The reference rate is the rate of double transitions.
Some base-pair substitutions are not allowed (null substitution rate).
The transition matrix for the RNA16A model is given in
RNA16A transition matrix