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     Full model name: Felsenstein 84, compatible with PHYLIP's dnaml.

     Model type: Nucleotide

     Model options:

  • Single Rate Class. Rates are homogeneous (same for all sites in the data).
  • Multiple Rate Classes Different sites may have different rates. The user specifies how many different rate classes there should be, provides rates for each class, and indicates the probability for each rate class.

     Independent Parameters: a (for each branch of the tree)

    Rate Matrix:

    with the vector representing nucleotide frequencies (proportions) from the data. '*' is defined to be the negative of the sum of all other row elements. 'R' is the transition/transversion ratio parameter in dnaml.

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