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

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.
Covarion model for Binary data

Inputs:

alpha, switchRate, vfrequencies, hfrequencies, mode, rates, eigenSystem, frequencies

 

alpha
type: beast.core.parameter.RealParameter
the rate of evolution in slow mode
Required input

 

switchRate
type: beast.core.parameter.RealParameter
the rate of flipping between slow and fast modes
Required input

 

vfrequencies
type: beast.core.parameter.RealParameter
the frequencies of the visible states
Required input

 

hfrequencies
type: beast.core.parameter.RealParameter
the frequencies of the hidden rates
Optional input

 

mode
type: beast.evolution.substitutionmodel.BinaryCovarion$MODE
one of BEAST, REVERSIBLE, TUFFLESTEEL BEAST = implementation as in BEAST 1 REVERSIBLE = like BEAST 1 implementation, but using frequencies to make it reversible TUFFLEYSTEEL = Tuffley & Steel (1996) impementation (no rates for
Optional input

 

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.
Optional 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
Optional input