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

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.
General Time Reversible model of nucleotide evolution. Rates that are not specified are assumed to be 1.

Inputs:

rateAC, rateAG, rateAT, rateCG, rateCT, rateGT, rates, eigenSystem, frequencies

 

rateAC
type: beast.core.Function
substitution rate for A to C (default 1)
Optional input

 

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

 

rateAT
type: beast.core.Function
substitution rate for A to T (default 1)
Optional input

 

rateCG
type: beast.core.Function
substitution rate for C to G (default 1)
Optional input

 

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

 

rateGT
type: beast.core.Function
substitution rate for G to T (default 1)
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