BEAST v2.5.0 Documentation: beast.evolution.substitutionmodel.GeneralSubstitutionModel

implemented by the following
beast.evolution.substitutionmodel.BinaryCovarion
beast.evolution.substitutionmodel.Blosum62
beast.evolution.substitutionmodel.CPREV
beast.evolution.substitutionmodel.Dayhoff
beast.evolution.substitutionmodel.GTR
beast.evolution.substitutionmodel.JTT
beast.evolution.substitutionmodel.MTREV
beast.evolution.substitutionmodel.SYM
beast.evolution.substitutionmodel.TIM
beast.evolution.substitutionmodel.TVM
beast.evolution.substitutionmodel.WAG

Specifies transition probability matrix with no restrictions on the rates other than that one of the is equal to one and the others are specified relative to this unit rate. Works for any number of states.

Inputs:

rates, eigenSystem, frequencies

 

rates
type: beast.core.Function
Rate parameter which defines the transition rate matrix. Only the off-diagonal entries need to be specified (diagonal makes row sum to zero in a rate matrix). Entry i specifies the rate from floor(i/(n-1)) to i%(n-1)+delta where n is the number of states and delta=1 if floor(i/(n-1)) <= i%(n-1) and 0 otherwise.
Required input

 

eigenSystem
type: java.lang.String
Name of the class used for creating an EigenSystem
Optional input. Default: beast.evolution.substitutionmodel.DefaultEigenSystem

 

frequencies
type: beast.evolution.substitutionmodel.Frequencies
substitution model equilibrium state frequencies
Required input