BEAST v2.5.0 Documentation: beast.evolution.likelihood.GenericTreeLikelihood

implemented by the following
beast.evolution.likelihood.BeagleTreeLikelihood
beast.evolution.likelihood.ThreadedTreeLikelihood
beast.evolution.likelihood.TreeLikelihood

BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Generic tree likelihood for an alignment given a generic SiteModel, a beast tree and a branch rate model

Logable: yes, this can be used in a log.

Inputs:

data, tree, siteModel, branchRateModel

 

data
type: beast.evolution.alignment.Alignment
sequence data for the beast.tree
Required input

 

tree
type: beast.evolution.tree.TreeInterface
phylogenetic beast.tree with sequence data in the leafs
Required input

 

siteModel
type: beast.evolution.sitemodel.SiteModelInterface
site model for leafs in the beast.tree
Required input

 

branchRateModel
type: beast.evolution.branchratemodel.BranchRateModel$Base
A model describing the rates on the branches of the beast.tree.
Optional input