BEAST v2.5.0 Documentation: beast.evolution.sitemodel.SiteModel

Defines mutation rate and gamma distributed rates across sites (optional) and proportion of the sites invariant (also optional).

Inputs:

mutationRate, gammaCategoryCount, shape, proportionInvariant, substModel

 

mutationRate
type: beast.core.parameter.RealParameter
mutation rate (defaults to 1.0)
Optional input

 

gammaCategoryCount
type: java.lang.Integer
gamma category count (default=zero for no gamma)
Optional input. Default: 0

 

shape
type: beast.core.parameter.RealParameter
shape parameter of gamma distribution. Ignored if gammaCategoryCount 1 or less
Optional input

 

proportionInvariant
type: beast.core.parameter.RealParameter
proportion of sites that is invariant: should be between 0 (default) and 1
Optional input

 

substModel
type: beast.evolution.substitutionmodel.SubstitutionModel
substitution model along branches in the beast.tree
Required input