Navigation Banner
 
  HyPhy Documentation: Miscellaneous: Rate distributions

      The following distributions are predefined. By default, HYPHY uses sampling by conditional mean.

  • Unit Mean Gamma.

    DENSITY
    MEAN
    VARIANCE
    PARAMETERS    

  • Beta.

    DENSITY
    MEAN
    VARIANCE
    PARAMETERS    

  • Normal (x>0).

    DENSITY
    MEAN
    VARIANCE
    PARAMETERS    

    where denotes the CDF of standard normal evaluated at x.

  • Log-Normal (x>0).

    DENSITY
    MEAN
    VARIANCE
    PARAMETERS    

  • Gamma+Inv (x>=0).

    DENSITY
    MEAN
    VARIANCE
    PARAMETERS    

  • Gamma Quadratures (x>0).

    Same distribution as the usual gamma, except that discretization is carried out using Gauss-Laguerre quadratures. This ensures, that for N rate classes, the first 2N-1 moments of the discretized distribution match those of the continuous distribution.
    Idea taken from: Felstenstein, J "Taking Variation of Evolutionary Rates Between Sites into Account in Inferring Phylogenies". J.Mol.Evol (2001) 53:447-455.

  • Inv Class.

    DENSITY
    MEAN
    VARIANCE
    PARAMETERS    

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