More complex models Hy-Phy has support for an infinite number of substitution models. Any time reversible model using any finite sequence alphabet can be used. Models for codon and amino acid sequences are available through the Standard Analyses menu selection. For now, we refer users who are interested in writing code for such alphabets to the files in the Examples subdirectory.
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002