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The content of this file is highly dependant on the substitution model used
and we cannot describe it in general terms. The fields
used to assign a value to each parameter are hopefully quite self-explanatory
as long as you know the underlying substitution model.
You might need to have a look at the transition matrices section
to understand the PHASE
concept of ``rate ratios'' in substitution models.
Each ``Rate ratio i'' parameter
in this file stands for the parameter in the transition matrix of the
corresponding model. Transition matrices for all implemented substitution models are given
there for DNA models and
there for RNA models.