BEAST v2.6.7 Documentation: beast.evolution.speciation.GeneTreeForSpeciesTreeDistribution

BEASTObject that performs calculations based on the State.
Probabilistic representation that can produce a log probability for instance for running an MCMC chain.
Distribution on a tree, typically a prior such as Coalescent or Yule
Calculates probability of gene tree conditioned on a species tree (multi-species coalescent)

Logable: yes, this can be used in a log.


speciesTree, ploidy, speciesTreePrior, treetop, tree, treeIntervals


type: beast.evolution.tree.TreeInterface
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: beast.evolution.speciation.SpeciesTreePopFunction
defines population function and its parameters
Required input


type: beast.evolution.speciation.TreeTopFinder
calculates height of species tree, required only for linear *beast analysis
Optional input


type: beast.evolution.tree.TreeInterface
tree over which to calculate a prior or likelihood
Required input


type: beast.evolution.tree.coalescent.TreeIntervals
Intervals for a phylogenetic beast tree
Either this, or tree needs to be specified