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

implemented by the following
beast.evolution.likelihood.BeagleTreeLikelihood

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
Calculates the probability of sequence data on a beast.tree given a site and substitution model using a variant of the 'peeling algorithm'. For details, seeFelsenstein, Joseph (1981). Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17 (6): 368-376.

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

Inputs:

useAmbiguities, useTipLikelihoods, implementation, scaling, data, tree, siteModel, branchRateModel

 

useAmbiguities
type: java.lang.Boolean
flag to indicate that sites containing ambiguous states should be handled instead of ignored (the default)
Optional input. Default: false

 

useTipLikelihoods
type: java.lang.Boolean
flag to indicate that partial likelihoods are provided at the tips
Optional input. Default: false

 

implementation
type: java.lang.String
name of class that implements this treelikelihood potentially more efficiently. This class will be tried first, with the TreeLikelihood as fallback implementation. When multi-threading, multiple objects can be created.
Optional input. Default: beast.evolution.likelihood.BeagleTreeLikelihood

 

scaling
type: beast.evolution.likelihood.TreeLikelihood$Scaling
type of scaling to use, one of [none, always, _default]. If not specified, the -beagle_scaling flag is used.
Optional input

 

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