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TreeTools (version 1.16.1)

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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Version

Install

install.packages('TreeTools')

Monthly Downloads

2,405

Version

1.16.1

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

August 24th, 2025

Functions in TreeTools (1.16.1)

Ancestors of an edge

Decompose additive (ordered) phylogenetic characters

DoubleFactorial

Double factorial

Drop leaves from tree

Construct consensus trees

Constrained neighbour-joining tree

Distance between edges

ConsensusWithout

Reduced consensus, omitting specified taxa

CompatibleSplits

Which splits are compatible?

DescendantEdges

Identify descendant edges

EnforceOutgroup

Generate a tree with a specified outgroup

Identify vertices retained when leaves are dropped

Add full stop to end of a sentence

Hamming distance between taxa in a phylogenetic dataset

Paths present in reduced tree

Robust universal tree balance index

Extract taxa from a matrix block

ImposeConstraint

Force a tree to match a constraint

Generate pectinate, balanced or random trees

Convert between matrices and phyDat objects

Data from Zhang et al. 2016

Minimum spanning tree

Most recent common ancestor

Match nodes and edges between trees

Check for mismatch between character vectors

Identify taxa with long branches

LeafLabelInterchange

Leaf label interchange

Generate binary tree by collapsing polytomies

Write Newick Tree

MorphoBankDecode

Decode MorphoBank text

Number of trees one SPR step away

Number of trees

Reorder edges of a phylogenetic tree

Number of distinct splits

Count descendants for each node in a tree

Number of leaves in a phylogenetic tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Generate a neighbour joining tree

PairwiseDistances

Distances between each pair of trees

Distance of each node from tree exterior

Number of edges incident to each node in a tree

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Read phylogenetic characters from file

Convert between strings and phyDat objects

Polarize splits on a single taxon

Calculate length of paths between each pair of vertices within tree

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

Renumber a tree's nodes and tips

Which node is a tree's root?

Renumber a tree's tips

Root or unroot a phylogenetic tree

Visualize position of rogue taxa

Reorder tree edges and nodes

Select element at random

RightmostCharacter

Rightmost character of string

Reweight phylogenetic characters

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Extract a subtree

Produce a legend for continuous gradient scales

Frequency of splits

Convert object to Splits

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

"Stemwardness" of a leaf

SplitMatchProbability

Probability of matching this well

SplitConsistent

Identify consistent / conflicting splits

Subset of a split on fewer leaves

Colour for node support value

Tips contained within splits

Is tree rooted?

TreeTools-package

Unique integer indices for bifurcating tree topologies

Display time-calibrated tree using tip information only

TotalCopheneticIndex

Total Cophenetic Index

Remove metadata from trees

Extract tip labels

Integer representing shape of a tree

WriteTntCharacters

Write morphological character matrix to TNT file

Write a phylogenetic tree in Newick format

Remove quotation marks from a string

Identify and remove trivial splits

Relative length of internal branches

Add tree to start of list

UnrootedTreesMatchingSplit

Number of trees consistent with split

Generate trivial trees

TreesMatchingTree

Number of trees containing a tree

TreesMatchingSplit

Number of trees matching a bipartition split

Efficiently convert edge matrix to splits

Is an object a TreeNumber object?

Convert object to multiPhylo class

Random parent vector

match,Splits,Splits-method

match,phylo,phylo-method

Brewer palettes

doubleFactorials

Double factorials

Number of rooted / unrooted tree shapes

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

sort.multiPhylo

Sort a list of phylogenetic trees

Exclusive OR operation

print.TreeNumber

Print TreeNumber object

logDoubleFactorials

Natural logarithms of double factorials

Wrapper for internal C function root_on_node()

CharacterInformation

Character information content

Convert phylogenetic tree to ClusterTable

Read modification time from "ape" Nexus file

Collapse nodes on a phylogenetic tree

Cladistic information content of a tree

ArtificialExtinction

Artificial Extinction

ClusterTable-methods

S3 methods for ClusterTable objects

Add a tip to a phylogenetic tree