| implemented by the following |
| beastclassic.evolution.substitutionmodel.SVSGeneralSubstitutionModel |
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
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.
rates, eigenSystem, frequencies
| 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 |