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##

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**
**GC** as a reference for the rate ratios.

**Subsections**

Gowri-Shankar Vivek
2003-04-24