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TreeTools (version 2.4.1)

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

2,387

Version

2.4.1

License

GPL (>= 3)

Issues

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Repository

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

Homepage

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

Maintainer

Martin R. Smith

Last Published

September 10th, 2026

Functions in TreeTools (2.4.1)

Generate pectinate, balanced or random trees

Add full stop to end of a sentence

ImposeConstraint

Force a tree to match a constraint

Ratio of external:internal edge length

Hamming distance between taxa in a phylogenetic dataset

Paths present in reduced tree

Distance between edges

Extract taxa from a matrix block

Robust universal tree balance index

Identify vertices retained when leaves are dropped

Generate binary tree by collapsing polytomies

LeafLabelInterchange

Leaf label interchange

Most recent common ancestor

Minimum spanning tree

Identify taxa with long branches

Data from Zhang et al. 2016

Match nodes and edges between trees

Check for mismatch between character vectors

Generate a neighbour joining tree

Convert between matrices and phyDat objects

Count descendants for each node in a tree

Write Newick Tree

Number of leaves in a phylogenetic tree

Number of distinct splits

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of trees

MorphoBankDecode

Decode MorphoBank text

Number of trees one SPR step away

NexusTokensToInteger

Convert Nexus token matrix to integer

PairwiseDistances

Distances between each pair of trees

Calculate length of paths between each pair of vertices within tree

Number of edges incident to each node in a tree

Colour a tree by topology

Polarize splits on a single taxon

Distance of each node from tree exterior

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

Convert between strings and phyDat objects

Reorder edges of a phylogenetic tree

Read phylogenetic characters from file

Renumber a tree's nodes and tips

Renumber a tree's tips

Visualize position of rogue taxa

Re-weight phylogenetic characters

Which node is a tree's root?

Reorder tree edges and nodes

RightmostCharacter

Rightmost character of string

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

SplitMatchProbability

Probability of matching this well

SplitConsistent

Identify consistent / conflicting splits

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Convert object to Splits

Frequency of splits

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Root or unroot a phylogenetic tree

"Stemwardness" of a leaf

Select element at random

Is tree rooted?

Tips contained within splits

Extract tip labels

Colour for node support value

Display time-calibrated tree using tip information only

Remove metadata from trees

TotalCopheneticIndex

Total Cophenetic Index

Extract a subtree

Subset of a split on fewer leaves

Unique integer indices for bifurcating tree topologies

UnrootedTreesMatchingSplit

Number of trees consistent with split

Relative length of internal branches

Remove quotation marks from a string

Identify and remove trivial splits

Add tree to start of list

TreesMatchingTree

Number of trees containing a tree

Integer representing shape of a tree

TreesMatchingSplit

Number of trees matching a bipartition split

TreeTools-package

Generate trivial trees

Efficiently convert edge matrix to splits

Is an object a TreeNumber object?

Convert object to multiPhylo class

Write a phylogenetic tree in Newick format

WriteTntCharacters

Write morphological character matrix to TNT file

doubleFactorials

Double factorials

Random parent vector

Brewer palettes

logDoubleFactorials

Natural logarithms of double factorials

match,Splits,Splits-method

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

sort.multiPhylo

Sort a list of phylogenetic trees

Wrapper for internal C function root_on_node()

print.TreeNumber

Print TreeNumber object

Exclusive OR operation

Number of rooted / unrooted tree shapes

match,phylo,phylo-method

Read modification time from "ape" Nexus file

Count cherries in a tree

Cladistic information content of a tree

ArtificialExtinction

Artificial Extinction

ClusterTable-methods

S3 methods for ClusterTable objects

Convert phylogenetic tree to ClusterTable

CharacterInformation

Character information content

DoubleFactorial

Double factorial

DescendantEdges

Identify descendant edges

Decompose additive (ordered) phylogenetic characters

Drop leaves from tree

ConsensusWithout

Reduced consensus, omitting specified taxa

Construct consensus trees

Add a tip to a phylogenetic tree

Ancestors of an edge

Constrained neighbour-joining tree

Collapse nodes on a phylogenetic tree

CompatibleSplits

Which splits are compatible?