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.
Frequencies for ModelTest model, can switch between equal and empricial/estimated frequencies
hasEqualFreqs, empirical, data, estimate, frequencies
| type: beast.base.inference.parameter.BooleanParameter |
| flag to indicate equal frequencies shouldbe used |
| Required input |
| type: java.lang.Boolean |
| flag for using empirical frequencies (if true), instead of estimated frequencies |
| Optional input. Default: true |
| type: beast.base.evolution.alignment.Alignment |
| Sequence data for which frequencies are calculated |
| Either this, or frequencies needs to be specified |
| 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 |
| type: beast.base.inference.parameter.RealParameter |
| A set of frequencies specified as space separated values summing to 1 |
| Either this, or data needs to be specified |