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TreeTools (version 2.0.0)

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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Install

install.packages('TreeTools')

Monthly Downloads

7,875

Version

2.0.0

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 23rd, 2025

Functions in TreeTools (2.0.0)

Decompose additive (ordered) phylogenetic characters

Construct consensus trees

ConsensusWithout

Reduced consensus, omitting specified taxa

Generate pectinate, balanced or random trees

Extract taxa from a matrix block

Paths present in reduced tree

Minimum spanning tree

Most recent common ancestor

Generate binary tree by collapsing polytomies

Number of distinct splits

Match nodes and edges between trees

Number of leaves in a phylogenetic tree

Identify vertices retained when leaves are dropped

ImposeConstraint

Force a tree to match a constraint

Convert between matrices and phyDat objects

Check for mismatch between character vectors

Reorder edges of a phylogenetic tree

Write Newick Tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of trees one SPR step away

MorphoBankDecode

Decode MorphoBank text

LeafLabelInterchange

Leaf label interchange

Count descendants for each node in a tree

Add full stop to end of a sentence

Data from Zhang et al. 2016

Distance between edges

PairwiseDistances

Distances between each pair of trees

Number of edges incident to each node in a tree

Generate a neighbour joining tree

Calculate length of paths between each pair of vertices within tree

Polarize splits on a single taxon

Read phylogenetic characters from file

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Identify taxa with long branches

Convert between strings and phyDat objects

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

Number of trees

Renumber a tree's tips

Visualize position of rogue taxa

Which node is a tree's root?

Select element at random

RightmostCharacter

Rightmost character of string

Reorder tree edges and nodes

Root or unroot a phylogenetic tree

Renumber a tree's nodes and tips

Reweight phylogenetic characters

Convert object to Splits

Extract a subtree

SplitsInBinaryTree

Maximum splits in an n-leaf tree

"Stemwardness" of a leaf

SplitConsistent

Identify consistent / conflicting splits

Colour for node support value

Frequency of splits

SplitMatchProbability

Probability of matching this well

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

Add tree to start of list

Relative length of internal branches

WriteTntCharacters

Write morphological character matrix to TNT file

TreeTools-package

Identify and remove trivial splits

Convert object to multiPhylo class

Is tree rooted?

TotalCopheneticIndex

Total Cophenetic Index

Write a phylogenetic tree in Newick format

Generate trivial trees

Random parent vector

match,Splits,Splits-method

match,phylo,phylo-method

Brewer palettes

Is an object a TreeNumber object?

Subset of a split on fewer leaves

Tips contained within splits

logDoubleFactorials

Natural logarithms of double factorials

Remove metadata from trees

Remove quotation marks from a string

Number of rooted / unrooted tree shapes

TreesMatchingTree

Number of trees containing a tree

TreesMatchingSplit

Number of trees matching a bipartition split

Extract tip labels

Wrapper for internal C function root_on_node()

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

Display time-calibrated tree using tip information only

doubleFactorials

Double factorials

print.TreeNumber

Print TreeNumber object

sort.multiPhylo

Sort a list of phylogenetic trees

Efficiently convert edge matrix to splits

UnrootedTreesMatchingSplit

Number of trees consistent with split

Exclusive OR operation

CharacterInformation

Character information content

ClusterTable-methods

S3 methods for ClusterTable objects

Cladistic information content of a tree

ArtificialExtinction

Artificial Extinction

Read modification time from "ape" Nexus file

Count cherries in a tree

Add a tip to a phylogenetic tree

Convert phylogenetic tree to ClusterTable

Ancestors of an edge

DoubleFactorial

Double factorial

Constrained neighbour-joining tree

Drop leaves from tree

DescendantEdges

Identify descendant edges

Collapse nodes on a phylogenetic tree

CompatibleSplits

Which splits are compatible?

Robust universal tree balance index

Hamming distance between taxa in a phylogenetic dataset