3.5 Process specification

The substitution model specification over the tree is set up in different parts.

nonhomogeneous = {no|one_per_branch|general}

Set the type of model. The no option is used for homogeneous models. The one_per_branch option is used as a short cut for setting branch models (for instance Galtier and Gouy 97 for branch GC content, or PAML branch model), and the general option for the more general case, including PAML clade models. In either of the last two cases, the model is potentially non-stationary, that is, possibly not at the equilibrium and hence includes the root frequencies as additional parameters. If the substitution model is not the same across the tree, then the model is also non-homogeneous.

In combination with those models, one can also specify a distribution of site-specific rate.