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.
Complex-diagonalizable, irreversible substitution model
SVS General Substitution Model
Edwards, C. J., Suchard, M. A., Lemey, P., ... & Valdiosera, C. E. (2011). Ancient hybridization and an Irish origin for the modern polar bear matriline. Current Biology, 21(15), 1251-1258.
rateIndicator, symmetric, rates, eigenSystem, frequencies
| type: beast.base.inference.parameter.BooleanParameter |
| rates to indicate the presence or absence of transition matrix entries |
| Required input |
| type: java.lang.Boolean |
| Indicates the rate matrix is symmetric. If true (default) n(n-1)/2 rates and indicators need to be specified. If false, n(n-1) rates and indicators need to be specified. |
| Optional input. Default: true |
| 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 |