MutationDefinition defines a common data structure for defining the whether
a mutation is annotated as a replacement or silent mutation.
name of the MutationDefinition.
description of the model and its source.
named character vectors with single-letter amino acid codes as names
and amino acid classes as values, with
NA assigned to set of
c("X", "*", "-", "."). Replacement (R) is be
defined as a change in amino acid class and silent (S) as no
change in class.
matrix of codons (columns) and substitutions (rows).
See MUTATION_SCHEMES for a set of predefined
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