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