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  HyPhy Documentation: Models: Aminoacid Models: Equal Input substitution model

     Full model name: Equal Input model for amino acids.

     Model type: Amino acids.

     Model options:

  • Fixed rates. . Rates are homogeneous (same for all sites in the data).
  • 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: a (for each branch of the tree) and, if rate variation is selected as an option, the corresponding distribution/hmm parameters.

    Rate Matrix Entries:

   i,j range from 1 to 20 and denote the ij cell denotes the instantaneous rate of change from amino acid i to amino acid j. Numerical ordering of the amino acids is based on the sorted alphabetical order of their one character abbreviations (see Amino acid character table).

    '*' is defined to be the negative of the sum of all other row elements.

  denotes the proportion of amino acid j as observed in the data.

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