BEAST v2.5.0 Documentation: beast.evolution.substitutionmodel.Frequencies

BEASTObject that performs calculations based on the State.
Represents character frequencies typically used as distribution of the root of the tree. Calculates empirical frequencies of characters in sequence data, or simply assumes a uniform distribution if the estimate flag is set to false.

Inputs:

data, estimate, frequencies

 

data
type: beast.evolution.alignment.Alignment
Sequence data for which frequencies are calculated
Either this, or frequencies needs to be specified

 

estimate
type: java.lang.Boolean
Whether to estimate the frequencies from data (true=default) or assume a uniform distribution over characters (false)
Optional input. Default: true

 

frequencies
type: beast.core.parameter.RealParameter
A set of frequencies specified as space separated values summing to 1
Either this, or data needs to be specified