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.
rateAG, rateCT, rateTransversions1, rateTransversions2, rates, eigenSystem, frequencies
| type: beast.core.parameter.RealParameter |
| substitution rate for A to G (default 1) |
| Optional input |
| type: beast.core.parameter.RealParameter |
| substitution rate for C to T (default 1) |
| Optional input |
| type: beast.core.parameter.RealParameter |
| substitution rate for A<->C and G<->T |
| Optional input |
| type: beast.core.parameter.RealParameter |
| substitution rate for C<->G and A<->T |
| Optional input |
| 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 |
| type: java.lang.String |
| Name of the class used for creating an EigenSystem |
| Optional input. Default: beast.evolution.substitutionmodel.DefaultEigenSystem |
| type: beast.evolution.substitutionmodel.Frequencies |
| substitution model equilibrium state frequencies |
| Required input |