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 |