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TreeTools (version 1.15.0)

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

1,996

Version

1.15.0

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

July 21st, 2025

Functions in TreeTools (1.15.0)

Identify vertices retained when leaves are dropped

Hamming distance between taxa in a phylogenetic dataset

Paths present in reduced tree

Robust universal tree balance index

Add full stop to end of a sentence

Drop leaves from tree

EnforceOutgroup

Generate a tree with a specified outgroup

MorphoBankDecode

Decode MorphoBank text

Convert between matrices and phyDat objects

Construct consensus trees

Check for mismatch between character vectors

Match nodes and edges between trees

Extract taxa from a matrix block

Generate pectinate, balanced or random trees

Number of leaves in a phylogenetic tree

Generate binary tree by collapsing polytomies

Minimum spanning tree

Write Newick Tree

Distance of each node from tree exterior

Reorder edges of a phylogenetic tree

Number of trees one SPR step away

Renumber a tree's nodes and tips

ImposeConstraint

Force a tree to match a constraint

Convert between strings and phyDat objects

Polarize splits on a single taxon

Data from Zhang et al. 2016

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

NPartitionPairs

Distributions of tips consistent with a partition pair

Read phylogenetic characters from file

Most recent common ancestor

Generate a neighbour joining tree

Reorder tree edges and nodes

Count descendants for each node in a tree

Renumber a tree's tips

Calculate length of paths between each pair of vertices within tree

PairwiseDistances

Distances between each pair of trees

Produce a legend for continuous gradient scales

Select element at random

Root or unroot a phylogenetic tree

Frequency of splits

RightmostCharacter

Rightmost character of string

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Reweight phylogenetic characters

Convert object to Splits

SplitMatchProbability

Probability of matching this well

Visualize position of rogue taxa

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Which node is a tree's root?

"Stemwardness" of a leaf

Number of edges incident to each node in a tree

Number of trees

Display time-calibrated tree using tip information only

Colour for node support value

LeafLabelInterchange

Leaf label interchange

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

Subset of a split on fewer leaves

Number of distinct splits

Write a phylogenetic tree in Newick format

Convert object to multiPhylo class

TotalCopheneticIndex

Total Cophenetic Index

Remove metadata from trees

Tips contained within splits

TreeTools-package

WriteTntCharacters

Write morphological character matrix to TNT file

Extract tip labels

Add tree to start of list

Integer representing shape of a tree

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

Wrapper for internal C function root_on_node()

match,Splits,Splits-method

Remove quotation marks from a string

UnrootedTreesMatchingSplit

Number of trees consistent with split

Is an object a TreeNumber object?

logDoubleFactorials

Natural logarithms of double factorials

Extract a subtree

TreesMatchingSplit

Number of trees matching a bipartition split

TreesMatchingTree

Number of trees containing a tree

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

sort.multiPhylo

Sort a list of phylogenetic trees

Is tree rooted?

Unique integer indices for bifurcating tree topologies

Identify and remove trivial splits

doubleFactorials

Double factorials

Exclusive OR operation

Generate trivial trees

Efficiently convert edge matrix to splits

match,phylo,phylo-method

Brewer palettes

Random parent vector

Convert phylogenetic tree to ClusterTable

Collapse nodes on a phylogenetic tree

Read modification time from "ape" Nexus file

ArtificialExtinction

Artificial Extinction

Ancestors of an edge

CompatibleSplits

Which splits are compatible?

Distance between edges

Cladistic information content of a tree

ClusterTable-methods

S3 methods for ClusterTable objects

CharacterInformation

Character information content

Add a tip to a phylogenetic tree

Decompose additive (ordered) phylogenetic characters

DoubleFactorial

Double factorial

DescendantEdges

Identify descendant edges

ConsensusWithout

Reduced consensus, omitting specified taxa

Constrained neighbour-joining tree