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Depending on the data to be analysed, the PHASE
package can be used with
a wide variety of DNA substitution models
or
RNAspecific basepaired 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.
Basepaired 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
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GowriShankar Vivek
20030424