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.
Reversible jump based substitution model that can jump between all reversible nucleotide substitution models
Substitution model for correlated evolution of discrete characters by reversible‐jump
Logable: yes, this can be used in a log.
symmetric, rateMask, modelSet, modelIndicator, rates, eigenSystem, frequencies
| type: java.lang.Boolean |
| force rates to be symmetric |
| Optional input. Default: false |
| type: beast.base.inference.parameter.BooleanParameter |
| Allows switching rates off by setting the associated mask entry to false, if not specified, the mask is ignored |
| Optional input |
| type: bmodeltest.evolution.substitutionmodel.NucleotideRevJumpSubstModel$ModelSet |
| Which set of models to choose, one of [allreversible, transitionTransversionSplit, namedSimple, namedExtended] |
| Optional input |
| type: beast.base.inference.parameter.IntegerParameter |
| number of the model to be used |
| Required input |
| type: beast.base.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 |
| type: java.lang.String |
| Name of the class used for creating an EigenSystem |
| Optional input. Default: beast.base.evolution.substitutionmodel.DefaultEigenSystem |
| type: beast.base.evolution.substitutionmodel.Frequencies |
| substitution model equilibrium state frequencies |
| Required input |