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  HyPhy Documentation: Models: Nucleotide Models: HKY85 with Two Gammas

     Full model name: Hasegawa et.al., 1985 with 2 rate variation parameters drawn from two independent unit gamma distributions.

    Model type: Nucleotide

     Model options:

The user selects how many classes transition rates and transversion rates shall have.

     Independent Parameters:

a - branch length, R - global transversion/transition rate, alpha - shape parameter of the unit gamma distribution of transversion rates, beta - shape parameter of the unit gamma distribution of transition rates.

    Rate Matrix:

    with the vector representing nucleotide frequencies (proportions) from the data. is distributed as unit gamma with shape parameter alpha, and is distributed as unit gamma with shape parameter beta. '*' is defined to be the negative of the sum of all other row elements.

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