BEAST v2.5.0 Documentation: beast.evolution.branchratemodel.UCRelaxedClockModel

Defines an uncorrelated relaxed molecular clock.

Reference:

Drummond AJ, Ho SYW, Phillips MJ, Rambaut A (2006) Relaxed Phylogenetics and Dating with Confidence. PLoS Biol 4(5): e88

doi:10.1371/journal.pbio.0040088

Inputs:

distr, rateCategories, numberOfDiscreteRates, rateQuantiles, tree, normalize, clock.rate

 

distr
type: beast.math.distributions.ParametricDistribution
the distribution governing the rates among branches. Must have mean of 1. The clock.rate parameter can be used to change the mean rate.
Required input

 

rateCategories
type: beast.core.parameter.IntegerParameter
the rate categories associated with nodes in the tree for sampling of individual rates among branches.
Either this, or rateQuantiles needs to be specified

 

numberOfDiscreteRates
type: java.lang.Integer
the number of discrete rate categories to approximate the rate distribution by. A value <= 0 will cause the number of categories to be set equal to the number of branches in the tree. (default = -1)
Optional input. Default: -1

 

rateQuantiles
type: beast.core.parameter.RealParameter
the rate quantiles associated with nodes in the tree for sampling of individual rates among branches.
Either this, or rateCategories needs to be specified

 

tree
type: beast.evolution.tree.Tree
the tree this relaxed clock is associated with.
Required input

 

normalize
type: java.lang.Boolean
Whether to normalize the average rate (default false).
Optional input. Default: false

 

clock.rate
type: beast.core.parameter.RealParameter
mean clock rate (defaults to 1.0)
Optional input