BEAST v2.5.0 Documentation: beast.util.ClusterTree

BEASTObject that performs calculations based on the State.
A node that can be part of the state.
Tree (the T in BEAST) representing gene beast.tree, species beast.tree, language history, or other time-beast.tree relationships among sequence data.
Create initial beast.tree by hierarchical clustering, either through one of the classic link methods or by neighbor joining. The following link methods are supported:
o single link,
o complete link,
o UPGMA=average link,
o mean link,
o centroid,
o Ward and
o adjusted complete link
o neighborjoining
o neighborjoining2 - corrects tree for tip data, unlike plain neighborjoining

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

Inputs:

clusterType, taxa, distance, clock.rate, initial, trait, taxonset, nodetype, estimate

 

clusterType
type: beast.util.ClusterTree$Type
type of clustering algorithm used for generating initial beast.tree. Should be one of [single, average, complete, upgma, mean, centroid, ward, adjcomplete, neighborjoining, neighborjoining2] (default average)
Optional input

 

taxa
type: beast.evolution.alignment.Alignment
alignment data used for calculating distances for clustering
Optional input

 

distance
type: beast.evolution.alignment.distance.Distance
method for calculating distance between two sequences (default Jukes Cantor)
Optional input

 

clock.rate
type: beast.core.parameter.RealParameter
the clock rate parameter, used to divide all divergence times by, to convert from substitutions to times. (default 1.0)
Optional input

 

initial
type: beast.evolution.tree.Tree
tree to start with
Optional input

 

trait
type: beast.evolution.tree.TraitSet***
trait information for initializing traits (like node dates) in the tree
Optional input

 

taxonset
type: beast.evolution.alignment.TaxonSet
set of taxa that correspond to the leafs in the tree
Optional input

 

nodetype
type: java.lang.String
type of the nodes in the beast.tree
Optional input. Default: beast.evolution.tree.Node

 

estimate
type: java.lang.Boolean
whether to estimate this item or keep constant to its initial value
Optional input. Default: true