RNA16A model

PHASE contains a general 16-state model (RNA16), however this model has $119 + 15$ 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 $\alpha_1$, a rate of double transversions $\alpha_2$, a mismatch $\leftrightarrow$non-mismatch transition rate $\alpha_3$ for transitions requiring only one substitution and a mismatch $\leftrightarrow$mismatch transition rate $\alpha_4$ 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 table 2.10.

Table 2.10: RNA16A transition matrix