| implemented by the following |
| beast.evolution.likelihood.BeagleTreeLikelihood |
| beast.evolution.likelihood.ThreadedTreeLikelihood |
| beast.evolution.likelihood.TreeLikelihood |
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
Logable: yes, this can be used in a log.
data, tree, siteModel, branchRateModel
| 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 |