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.
Uses Beagle library to calculate Tree likelihood
Logable: yes, this can be used in a log.
useAmbiguities, useTipLikelihoods, implementation, scaling, rootFrequencies, data, tree, siteModel, branchRateModel
 
type: java.lang.Boolean |
flag to indicate that sites containing ambiguous states should be handled instead of ignored (the default) |
Optional input. Default: false |
 
type: java.lang.Boolean |
flag to indicate that partial likelihoods are provided at the tips |
Optional input. Default: false |
 
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 |
 
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 |
 
type: beast.evolution.substitutionmodel.Frequencies |
prior state frequencies at root, optional |
Optional input |
 
type: beast.evolution.alignment.Alignment |
sequence data for the beast.tree |
Required input |
 
type: beast.evolution.tree.TreeInterface |
phylogenetic beast.tree with sequence data in the leafs |
Required input |
 
type: beast.evolution.sitemodel.SiteModelInterface |
site model for leafs in the beast.tree |
Required input |
 
type: beast.evolution.branchratemodel.BranchRateModel$Base |
A model describing the rates on the branches of the beast.tree. |
Optional input |