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     Full model name: Goldman-Yang 1994

     Model type: Codon.

     Model options:

  • S/N independent Rates are homogeneous (same for all sites in the data). Each branch has 2 parameters (synonymous and non-synonymous rate).
  • S/N shared Rates are homogeneous (same for all sites in the data). Each branch has 1 parameters (non-synonymous rate). Synonymous/Non-synonymous ratio is shared by all branches in the tree.
  • S/N independent +Gamma Different sites may have different rates. The user specifies how many different rate classes there should be. Gamma distribution with unknown shape parameter alpha is used to evaluate rates for each class. The shape parameter of the gamma distribution is estimated as a model parameter. Each branch has 2 parameters (synonymous and non-synonymous rate).
  • S/N shared +Gamma Different sites may have different rates. The user specifies how many different rate classes there should be. Gamma distribution with unknown shape parameter alpha is used to evaluate rates for each class. The shape parameter of the gamma distribution is estimated as a model parameter. Each branch has 1 parameters (non-synonymous rate). Synonymous/Non-synonymous ratio is shared by all branches in the tree.

     Independent Parameters:

  • S/N independent mu - non-synonymous rate, R - Synonymous/Non-synonymous ratio for the branch; (for each branch); kappa - transition/transversion ratio (shared by all branches).
  • S/N shared mu - non-synonymous rate (for each branch); R - Synonymous/Non-synonymous ratio; kappa - transition/transversion ratio (shared by all branches).
  • S/N independent+Gamma mu - non-synonymous rate, R - Synonymous/Non-synonymous ratio for the branch; (for each branch); kappa - transition/transversion ratio (shared by all branches). alpha - the shape parameter of the gamma distribution (shared by all branches in the tree).
  • S/N shared +Gamma mu - non-synonymous rate (for each branch); R - Synonymous/Non-synonymous ratio; kappa - transition/transversion ratio (shared by all branches). alpha - the shape parameter of the gamma distribution (shared by all branches in the tree).

 

    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).

     Example of one-step changes: ACC->ATC (transition), ACC->AGC (transversion); more than one step: ACC->CGC. refers to the equilibrium frequency of codon j.

      Equilibrium frequencies of codons:

  •  GY94:

    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.

  • GY94w9:

    Equilibrium frequency of codon ijk is the product of observed frequencies of nucleotides which compose the codon, which are tabulated by 1st,2nd and 3rd positions in the codon (i.e. 3 sets of 4 frequencies are used, one for each position in the codon), normalized by a factor to account for the presence of stop codons.

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