BEAST v2.5.0 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.

Inputs:

speciesTree, ploidy, speciesTreePrior, treetop, tree, treeIntervals

 

speciesTree
type: beast.evolution.tree.TreeInterface
species tree containing the associated gene tree
Required input

 

ploidy
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

 

speciesTreePrior
type: beast.evolution.speciation.SpeciesTreePrior
defines population function and its parameters
Required input

 

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

 

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

 

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