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     Full model name: Muse-Gaut 1994 with rate matrix extensions.

     Model type: Codon.

     Model options:

  • Rate matrix options. The user selects the type of nucleotide rate multipliers to graft onto the MG94 rate matrix (see example below). The specification is done the same way as in the Custom 4x4 model. This step may add up to 5 shared rate parameters (depending on the user's choice: B,C,D,E,F) to the model, to compensate for nucleotide substitution bias, which may not be accounted for in the classic MG94.
  • Local. Rates are homogeneous (same for all sites in the data). Each branch has 2 parameters (synonymous and non-synonymous rate).
  • Global. Rates are homogeneous (same for all sites in the data). Each branch has 1 parameter (synonymous rate). Non-Synonymous/Synonymous ratio is shared by all branches in the tree.
  • Global+Variation Each branch has 1 parameter (synonymous rate). Non-Synonymous/Synonymous ratio is shared by all branches in the tree. Different sites may have different rates. The user specifies how many different rate classes there should and selects one of the available distributions to be sampled. Distribution parameters are estimated.
  • Rate Variation+HM. Similar to Rate Variation except that rates at adjacent sites are correlated via a Hidden Markov Model

     Independent Parameters (in addition to nucleotide rate substitution shared parameters):

  • Local. synRate - synonymous rate, nonSynRate - non-synonymous rate; (for each branch)
  • Global. synRate - synonymous rate (for each branch); R - Non-synonymous/Synonymous ratio (shared by all branches in the tree).
  • Rate Variation (+HM). Same as in the global setting plus the appropriate distribution parameters.

    Rate Matrix Entries. Example with 010010 (HKY85) nucleotide rates.

    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).

  • Local.

  • Global, Rate Variation (+HM) :

      Example of a one-step change (transition): 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, 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