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TreeTools (version 2.1.0)

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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Version

Install

install.packages('TreeTools')

Monthly Downloads

1,999

Version

2.1.0

License

GPL (>= 3)

Issues

Pull Requests

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Repository

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

Homepage

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

Maintainer

Martin R. Smith

Last Published

February 11th, 2026

Functions in TreeTools (2.1.0)

CharacterInformation

Character information content

Match nodes and edges between trees

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of trees

Number of distinct splits

Reorder edges of a phylogenetic tree

Write Newick Tree

MorphoBankDecode

Decode MorphoBank text

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Number of trees one SPR step away

Number of leaves in a phylogenetic tree

Number of edges incident to each node in a tree

Polarize splits on a single taxon

Count descendants for each node in a tree

Read phylogenetic characters from file

Generate a neighbour joining tree

PairwiseDistances

Distances between each pair of trees

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

Distance of each node from tree exterior

Calculate length of paths between each pair of vertices within tree

Convert between strings and phyDat objects

RightmostCharacter

Rightmost character of string

Root or unroot a phylogenetic tree

Visualize position of rogue taxa

Renumber a tree's tips

Select element at random

Which node is a tree's root?

Renumber a tree's nodes and tips

Reorder tree edges and nodes

Reweight phylogenetic characters

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Convert object to Splits

Subset of a split on fewer leaves

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

SplitMatchProbability

Probability of matching this well

SplitConsistent

Identify consistent / conflicting splits

"Stemwardness" of a leaf

Extract a subtree

Colour for node support value

Frequency of splits

Unique integer indices for bifurcating tree topologies

TotalCopheneticIndex

Total Cophenetic Index

Extract tip labels

Tips contained within splits

Display time-calibrated tree using tip information only

Relative length of internal branches

Remove metadata from trees

Is tree rooted?

TreeTools-package

Integer representing shape of a tree

Remove quotation marks from a string

UnrootedTreesMatchingSplit

Number of trees consistent with split

Write a phylogenetic tree in Newick format

Generate trivial trees

Identify and remove trivial splits

Add tree to start of list

TreesMatchingSplit

Number of trees matching a bipartition split

Convert object to multiPhylo class

WriteTntCharacters

Write morphological character matrix to TNT file

TreesMatchingTree

Number of trees containing a tree

Is an object a TreeNumber object?

match,Splits,Splits-method

print.TreeNumber

Print TreeNumber object

Efficiently convert edge matrix to splits

logDoubleFactorials

Natural logarithms of double factorials

match,phylo,phylo-method

Brewer palettes

doubleFactorials

Double factorials

Number of rooted / unrooted tree shapes

Random parent vector

Exclusive OR operation

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

Wrapper for internal C function root_on_node()

sort.multiPhylo

Sort a list of phylogenetic trees

Count cherries in a tree

Convert phylogenetic tree to ClusterTable

ClusterTable-methods

S3 methods for ClusterTable objects

Read modification time from "ape" Nexus file

ArtificialExtinction

Artificial Extinction

Cladistic information content of a tree

Construct consensus trees

Add a tip to a phylogenetic tree

DoubleFactorial

Double factorial

DescendantEdges

Identify descendant edges

Collapse nodes on a phylogenetic tree

Decompose additive (ordered) phylogenetic characters

Drop leaves from tree

ConsensusWithout

Reduced consensus, omitting specified taxa

Constrained neighbour-joining tree

Ancestors of an edge

CompatibleSplits

Which splits are compatible?

Identify vertices retained when leaves are dropped

Robust universal tree balance index

Paths present in reduced tree

ImposeConstraint

Force a tree to match a constraint

Hamming distance between taxa in a phylogenetic dataset

Add full stop to end of a sentence

Distance between edges

Identify taxa with long branches

Generate binary tree by collapsing polytomies

Data from Zhang et al. 2016

Most recent common ancestor

Minimum spanning tree

LeafLabelInterchange

Leaf label interchange

Generate pectinate, balanced or random trees

Extract taxa from a matrix block

Check for mismatch between character vectors

Convert between matrices and phyDat objects