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 $\leftrightarrow$G transitition is used as a reference by PHASE , $\alpha_{AG} = \alpha_{GA} = 1$.