Calculates the functionality of a single gene
GetFunctionality(gene.length, aa.data, optimal.aa, alpha, beta, gamma,
gp = NULL, aa.properties = NULL)Indicates the length of the gene used to calculate functionality.
A matrix of amino acids
A vector of inferred optimal amino acids.
The inferred Grantham composition paramter
The inferred Grantham polarity parameter
The inferred Grantham molecular volume parameter
A vector of gamma rates for calculating among site hetergeneity in functionality.
User-supplied amino acid distance properties. By default we assume Grantham (1974) properties.
The purpose of this function is to provide the functionality of a gene based on the inferred parameters from SelAC. The functionality is often used to scale phi.