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).
Wrapper around TreeParser to enable reading newick strings from files.
Logable: yes, this can be used in a log.
fileName, treeIndex, IsLabelledNewick, taxa, newick, offset, threshold, singlechild, adjustTipHeights, scale, binarizeMultifurcations, initial, trait, taxonset, nodetype, adjustTreeNodeHeights, estimate
| type: java.lang.String |
| Name of file containing tree in Newick format. |
| Required input |
| type: java.lang.Integer |
| Index of tree in tree file (default 0). |
| Optional input. Default: 0 |
| type: java.lang.Boolean |
| Is the newick tree labelled (alternatively contains node numbers)? Default=false. |
| Optional input. Default: false |
| type: beast.base.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.base.evolution.tree.Tree |
| tree to start with |
| Optional input |
| type: beast.base.evolution.tree.TraitSet*** |
| trait information for initializing traits (like node dates) in the tree |
| Optional input |
| type: beast.base.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.base.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 |