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     Full model name: Any of the reversible 4x4 models.

     Model type: Nucleotide

     Model options:

         Custom models are defined by means of a 6 character string which is is shorthand for defining 6 rate matrix elements which are located above the diagonal, left to right, top to bottom. The symbols in the string should be from the set '0','1','2','3','4','5'. If the two symbols in the string are identical, then the two corresponding entries of the rate matrix will be the same (see example below). Each model has the following options:

  • Local. Rates are homogeneous (same for all sites in the data). Each branch as many parameters as there are different characters in the model string.
  • Global. Rates are homogeneous (same for all sites in the data). Each branch one parameters, there are several shared ratios for the tree (the number of ratios is the same as the number of different characters in the model string less one).
  • Rate Variation. 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:

        Will depend on the model string. See the following Example.

     Example: Model string 012134

     Rate Matrix:

  • Local.

    5 independent parameters per branch: a,b,c,d,e.

  • Rate Variation, Rate Variation+HM:

    1 independent parameter per branch: t. 4 shared ratios: B,C,D,E.

    with the vector representing equilibrium nucleotide frequencies. '*' is defined to be the negative of the sum of all other row elements.

      Equilibrium frequencies. There are 3 options to choose from:

  • Observed: The proportions of nucleotides from the data will be used.
  • Equal: All frequencies are set to .25.
  • Custom: The user specifies the frequencies for each nucleotide.

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