BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Calculates the likelihood 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.
data, tree, siteModel, branchRateModel, useAmbiguities
| type: beast.base.evolution.alignment.Alignment |
| sequence data for the beast.tree |
| Required input |
| type: beast.base.evolution.tree.Tree |
| phylogenetic beast.tree with sequence data in the leafs |
| Required input |
| type: beast.base.evolution.sitemodel.SiteModelInterface$Base |
| site model for leafs in the beast.tree |
| Required input |
| type: beast.base.evolution.branchratemodel.BranchRateModel$Base |
| A model describing the rates on the branches of the beast.tree. |
| Optional input |
| type: java.lang.Boolean |
| flag to indicate leafs that sites containing ambigue states should be handled instead of ignored (the default) |
| Optional input. Default: false |