BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Calculates probability of gene tree conditioned on a species tree (multi-species coalescent)
Logable: yes, this can be used in a log.
tree, treeIntervals, speciesTree, ploidy, sampling, speciesTreePrior, populationModel, taxonset
| type: beast.base.evolution.tree.TreeInterface |
| tree over which to calculate a prior or likelihood |
| Required input |
| type: beast.base.evolution.tree.TreeIntervals |
| Intervals for a phylogenetic beast tree |
| Either this, or tree needs to be specified |
| type: starbeast3.tree.SpeciesTree |
| species tree containing the associated gene tree |
| Required input |
| type: java.lang.Double |
| ploidy (copy number) for this gene, typically a whole number or half (default 2 for autosomal_nuclear) |
| Optional input. Default: 2.0 |
| type: java.lang.Boolean |
| Set to true if using this class for simulating sequences |
| Optional input. Default: false |
| type: starbeast3.evolution.speciation.SpeciesTreePrior |
| defines population function and its parameters |
| Optional input |
| type: starbeast3.evolution.speciation.PopulationModel |
| Population model used to infer the multispecies coalescent probability for this gene |
| Optional input |
| type: beast.base.evolution.alignment.TaxonSet |
| set of taxa mapping lineages to species |
| Optional input |