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TreeTools (version 1.13.1)

Create, Modify and Analyse Phylogenetic Trees

Description

Efficient implementations of functions for the creation, modification and analysis of phylogenetic trees. Applications include: generation of trees with specified shapes; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) ; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2022) , and of tree balance (Mir et al. 2013, Lemant et al. 2022) , ; artificial extinction (Asher & Smith, 2022) ; import and export of trees from Newick, Nexus (Maddison et al. 1997) , and TNT formats; and analysis of splits and cladistic information.

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Install

install.packages('TreeTools')

Monthly Downloads

1,384

Version

1.13.1

License

GPL (>= 3)

Issues

Pull Requests

Stars

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Repository

https://github.com/ms609/TreeTools/

Homepage

https://ms609.github.io/TreeTools/

Maintainer

Martin R. Smith

Last Published

April 7th, 2025

Functions in TreeTools (1.13.1)

CompatibleSplits

Which splits are compatible?

DoubleFactorial

Double factorial

Ancestors of an edge

EnforceOutgroup

Generate a tree with a specified outgroup

Hamming distance between taxa in a phylogenetic dataset

Add full stop to end of a sentence

Paths present in reduced tree

Identify vertices retained when leaves are dropped

Robust universal tree balance index

ImposeConstraint

Force a tree to match a constraint

Extract taxa from a matrix block

Generate pectinate, balanced or random trees

MorphoBankDecode

Decode MorphoBank text

Data from Zhang et al. 2016

LeafLabelInterchange

Leaf label interchange

Number of trees one SPR step away

Most recent common ancestor

Generate binary tree by collapsing polytomies

Match nodes and edges between trees

Convert between matrices and phyDat objects

Minimum spanning tree

Write Newick Tree

Reorder edges of a phylogenetic tree

Numeric index of each node in a tree NodeNumbers() returns a sequence corresponding to the nodes in a tree

Generate a neighbour joining tree

Number of leaves in a phylogenetic tree

Count descendants for each node in a tree

Number of distinct splits

NPartitionPairs

Distributions of tips consistent with a partition pair

Distance of each node from tree exterior

Number of trees

Renumber a tree's tips

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Number of edges incident to each node in a tree

Renumber a tree's nodes and tips

Convert between strings and phyDat objects

PairwiseDistances

Distances between each pair of trees

Calculate length of paths between each pair of vertices within tree

Read phylogenetic characters from file

Polarize splits on a single taxon

Frequency of splits

Reorder tree edges and nodes

Visualize position of rogue taxa

Which node is a tree's root?

Produce a legend for continuous gradient scales

Root or unroot a phylogenetic tree

RightmostCharacter

Rightmost character of string

Select element at random

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Subset of a split on fewer leaves

"Stemwardness" of a leaf

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Extract tip labels

Extract a subtree

Colour for node support value

Convert object to Splits

Tips contained within splits

SplitMatchProbability

Probability of matching this well

Display time-calibrated tree using tip information only

TreeTools-package

Remove metadata from trees

Generate trivial trees

Unique integer indices for bifurcating tree topologies

Identify and remove trivial splits

Is tree rooted?

TreesMatchingSplit

Number of trees matching a bipartition split

TreesMatchingTree

Number of trees containing a tree

TotalCopheneticIndex

Total Cophenetic Index

Integer representing shape of a tree

Brewer palettes

Write a phylogenetic tree in Newick format

Remove quotation marks from a string

doubleFactorials

Double factorials

Random parent vector

Efficiently convert edge matrix to splits

UnrootedTreesMatchingSplit

Number of trees consistent with split

Add tree to start of list

WriteTntCharacters

Write morphological character matrix to TNT file

Convert object to multiPhylo class

Number of rooted / unrooted tree shapes

Is an object a TreeNumber object?

match,Splits,Splits-method

sort.multiPhylo

Sort a list of phylogenetic trees

Apply a function that returns 64-bit integers over a list or vector

Exclusive OR operation

print.TreeNumber

Print TreeNumber object

Wrapper for internal C function root_on_node()

match,phylo,phylo-method

logDoubleFactorials

Natural logarithms of double factorials

Cladistic information content of a tree

Read modification time from "ape" Nexus file

ClusterTable-methods

S3 methods for ClusterTable objects

Convert phylogenetic tree to ClusterTable

Add a tip to a phylogenetic tree

Collapse nodes on a phylogenetic tree

Decompose additive (ordered) phylogenetic characters

CharacterInformation

Character information content

Construct consensus trees

ConsensusWithout

Reduced consensus, omitting specified taxa

DescendantEdges

Identify descendant edges

ArtificialExtinction

Artificial Extinction

Distance between edges

Drop leaves from tree

Constrained neighbour-joining tree