BEAST v2.6.7 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.


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


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


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


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


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


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


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


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


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


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


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


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


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


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


type: java.lang.Boolean
if true (default), then tree node heights are adjusted to avoid non-positive branch lengths. If you want to maintain zero branch lengths then you must set this to false.
Optional input. Default: true


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