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.
Ancestral State Tree Likelihood
Reconstructs sequences at internal nodes and logs them in NEXUS format
Logable: yes, this can be used in a log.
logIndividualSites, tag, useMAP, returnML, useJava, sampleTips, leaftrait, useAmbiguities, useTipLikelihoods, implementation, scaling, rootFrequencies, data, tree, siteModel, branchRateModel
| type: java.lang.Boolean |
| if true, tree log gets one entry for every site, if false complete sequence is logged |
| Optional input. Default: false |
| type: java.lang.String |
| label used to report trait |
| Required input |
| type: java.lang.Boolean |
| whether to use maximum aposteriori assignments or sample |
| Optional input. Default: false |
| type: java.lang.Boolean |
| report integrate likelihood of tip data |
| Optional input. Default: true |
| type: java.lang.Boolean |
| prefer java, even if beagle is available |
| Optional input. Default: true |
| type: java.lang.Boolean |
| if tips have missing data/ambigous values sample them for logging (default true) |
| Optional input. Default: true |
| type: beastclassic.evolution.likelihood.LeafTrait*** |
| list of leaf traits |
| Optional input |
| 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.base.evolution.likelihood.BeagleTreeLikelihood |
| type: beast.base.evolution.likelihood.TreeLikelihood$Scaling |
| type of scaling to use, one of [none, always, _default]. If not specified, the -beagle_scaling flag is used. |
| Optional input |
| type: beast.base.evolution.substitutionmodel.Frequencies |
| prior state frequencies at root, optional |
| Optional input |
| type: beast.base.evolution.alignment.Alignment |
| sequence data for the beast.tree |
| Required input |
| type: beast.base.evolution.tree.TreeInterface |
| phylogenetic beast.tree with sequence data in the leafs |
| Required input |
| type: beast.base.evolution.sitemodel.SiteModelInterface |
| site model for leafs in the beast.tree |
| Required input |
| type: beast.base.evolution.branchratemodel.BranchRateModel$Base |
| A model describing the rates on the branches of the beast.tree. |
| Optional input |