BEAST v2.5.0 Documentation: beast.util.TreeParser

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 beast.tree by parsing from a specification of a beast.tree in Newick format (includes parsing of any meta data in the Newick string).

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

Inputs:

IsLabelledNewick, taxa, newick, offset, threshold, singlechild, adjustTipHeights, scale, binarizeMultifurcations, initial, trait, taxonset, nodetype, estimate

 

IsLabelledNewick
type: java.lang.Boolean
Is the newick tree labelled (alternatively contains node numbers)? Default=false.
Optional input. Default: false

 

taxa
type: beast.evolution.alignment.Alignment
Specifies the list of taxa represented by leaves in the beast.tree
Optional input

 

newick
type: java.lang.String
initial beast.tree represented in newick format
Optional input

 

offset
type: java.lang.Integer
offset if numbers are used for taxa (offset=the lowest taxa number) default=1
Optional input. Default: 1

 

threshold
type: java.lang.Double
threshold under which node heights (derived from lengths) are set to zero. Default=0.
Optional input. Default: 0.0

 

singlechild
type: java.lang.Boolean
flag to indicate that single child nodes are allowed. Default=true.
Optional input. Default: true

 

adjustTipHeights
type: java.lang.Boolean
flag to indicate if tipHeights shall be adjusted when date traits missing. Default=true.
Optional input. Default: true

 

scale
type: java.lang.Double
scale used to multiply internal node heights during parsing. Useful for importing starting from external programs, for instance, RaxML tree rooted using Path-o-gen.
Optional input. Default: 1.0

 

binarizeMultifurcations
type: java.lang.Boolean
Whether or not to turn multifurcations into sequences of bifurcations. (Default true.)
Optional input. Default: true

 

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