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.
Logs internal states sampled from the distribution at the MRCA of a set of taxa
Logable: yes, this can be used in a log.
taxonset, value, logParent, logMRCA, useAmbiguities, useTipLikelihoods, implementation, scaling, rootFrequencies, data, tree, siteModel, branchRateModel
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa defining a clade. The MRCA node of the clade is logged |
| Required input |
| type: java.lang.String |
| space delimited set of labels, one for each site in the alignment. Used as site label in the log file. |
| Optional input |
| type: java.lang.Boolean |
| flag to indicate the parent value should be logged |
| Optional input. Default: false |
| type: java.lang.Boolean |
| flag to indicate the MRCA value should be logged |
| Optional input. Default: true |
| 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 |