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  HyPhy Documentation: Models: Codon Models: MG94 with independent rate variation

     Full model name: Muse-Gaut 1994 with independent rate variation.

     Model type: Codon.

     Model options:

     The user specifies the number of rate classes for synonymous rates, and the number of rate classes for non-synonymous rates.

     Independent Parameters:

     t - branch length, R- non-synonymous to synonymous ratio, or to be more precise, the ratio of mean non-syn to mean syn rate (shared by all branches), alpha - the shape parameter for the unit mean gamma distribution of synonymous rates (shared by all branches), beta - the shape parameter for the unit mean gamma distribution of synonymous rates (shared by all branches).

    Rate Matrix Entries:

    Note: the rate matrix will have the same dimension as the number of non-stop codons in the genetic code which is being used be the analysis (61 for Universal Code).


       c,d are distributed (independently) as unit mean gammas, with shape parameters alpha and beta, respectively.

      Example of a one-step change: ACC->ATC; more than one step: ACC->CGC. refers to the observed frequency of the target nucleotide that is changed in transition from i to j. (E.g. it is the frequency of T in the example above).

      Equilibrium frequencies of codons:

     Equilibrium frequency of codon ijk is the product of observed frequencies of nucleotides which compose the codon, normalized by a factor to account for the presence of stop codons.

 
Sergei L. Kosakovsky Pond and Spencer V. Muse, 1997-2002