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Nucleotide substitution models implemented in *PHASE*

One can refer to Whelan et al. (2001) for a comprehensive review of
the following substitution models and their hierarchical relationships.
The transition rate matrices of these models can highlight
their differences. They are presented by increasing complexity, *i.e.*,
ordered according to their number of free parameters.
(equilibrium frequencies and/or rates). In nucleotide substitution
models, the A
G transitition is used as a reference by *PHASE*
,
.

**Subsections**

Gowri-Shankar Vivek
2003-04-24