Base-paired substitution models implemented in PHASE

Like DNA models, RNA substitution models are Markov models but they consider pairs of nucleotides as their elementary states rather than single sites. The PHASE software contains 16-state models to account for the 16 possible pairs that can be formed with 4 bases. These models have a lot of parameters and you might prefer them the 6-state and 7-state models where mismatch pairs are respectively discarded or lumped into a single state MM. The time-reversibility contraint and the average mutation rate are set as they were for DNA models. One can refer to Savill et al. (2001) for a better review of the following substitution models and their hierarchical relationships. With base-paired models, PHASE uses the rate of the double transition AU $\leftrightarrow$GC as a reference for the rate ratios.