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

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.
Transition model of nucleotide evolution (variable transition rates, two transversion rates). Rates that are not specified are assumed to be 1.

Inputs:

rateAG, rateCT, rateTransversions1, rateTransversions2, rates, eigenSystem, frequencies

 

rateAG
type: beast.core.parameter.RealParameter
substitution rate for A to G (default 1)
Optional input

 

rateCT
type: beast.core.parameter.RealParameter
substitution rate for C to T (default 1)
Optional input

 

rateTransversions1
type: beast.core.parameter.RealParameter
substitution rate for A<->C and G<->T
Optional input

 

rateTransversions2
type: beast.core.parameter.RealParameter
substitution rate for C<->G and A<->T
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
Required input