BEAST v2.6.7 Documentation: beast.evolution.substitutionmodel.Dayhoff

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.
A substitution model where the rates and frequencies are obtained from empirical evidence. Especially, amino acid models like WAG.
Dayhoff model for amino acid evolution Dayhoff, M.O., Schwartz, R.M., Orcutt, B.C. (1978) A model of evolutionary change in proteins. Dayhoff, M.O. (ed.) Atlas of Protein Sequence Structur., Vol5, Suppl. 3, National Biomedical Research Foundation, Washington DC, pp. 345-352.


rates, eigenSystem, frequencies


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
Optional input