Simple substitution model

Depending on the data to be analysed, the PHASE package can be used with a wide variety of DNA substitution models or RNA-specific base-paired models.

The content of the MODEL block is the same for all these models and the parameters are:

Model: the model's name, by convention it should be all upper case.
Model = REV
Nucleotide substitution models implemented include JC69, K80, HKY85, TN93 and REV. Base-paired substitution models implemented include RNA6A, RNA6B, RNA7A, RNA7D, RNA16A.

Discrete gamma distribution of rates: the discrete gamma model can be used to account for among site rate variation. Use yes/no values to turn this option on/off. When a discrete gamma model is used, PHASE expects the number of gamma categories to be specified. By default the discrete gamma model is not used.
Discrete gamma distribution of rates = yes

Number of gamma categories: when the discrete gamma model is used, you have to provide an integer to specify the desired number of discrete gamma categories.
Number of gamma categories = 5

Invariant sites: alternatively, or in conjunction with the discrete gamma model, the user can allow a proportion of sites to be invariant, i.e., with zero rate of evolution. The default value is no.
Invariant sites = yes