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TreeTools (version 1.14.0)

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

1,855

Version

1.14.0

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

May 13th, 2025

Functions in TreeTools (1.14.0)

DescendantEdges

Identify descendant edges

Decompose additive (ordered) phylogenetic characters

DoubleFactorial

Double factorial

Drop leaves from tree

ConsensusWithout

Reduced consensus, omitting specified taxa

Constrained neighbour-joining tree

Construct consensus trees

CompatibleSplits

Which splits are compatible?

Ancestors of an edge

Distance between edges

Hamming distance between taxa in a phylogenetic dataset

Robust universal tree balance index

Add full stop to end of a sentence

Extract taxa from a matrix block

Identify vertices retained when leaves are dropped

Generate pectinate, balanced or random trees

Paths present in reduced tree

ImposeConstraint

Force a tree to match a constraint

Minimum spanning tree

Number of trees one SPR step away

MorphoBankDecode

Decode MorphoBank text

EnforceOutgroup

Generate a tree with a specified outgroup

Match nodes and edges between trees

Count descendants for each node in a tree

Generate a neighbour joining tree

Generate binary tree by collapsing polytomies

Number of leaves in a phylogenetic tree

LeafLabelInterchange

Leaf label interchange

Number of distinct splits

Renumber a tree's nodes and tips

Renumber a tree's tips

Number of edges incident to each node in a tree

Calculate length of paths between each pair of vertices within tree

PairwiseDistances

Distances between each pair of trees

Convert between strings and phyDat objects

Write Newick Tree

Most recent common ancestor

Read phylogenetic characters from file

Polarize splits on a single taxon

Reorder edges of a phylogenetic tree

Which node is a tree's root?

Visualize position of rogue taxa

Data from Zhang et al. 2016

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

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Frequency of splits

Distance of each node from tree exterior

Convert between matrices and phyDat objects

Reorder tree edges and nodes

RightmostCharacter

Rightmost character of string

Produce a legend for continuous gradient scales

Subset of a split on fewer leaves

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Display time-calibrated tree using tip information only

Tips contained within splits

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of trees

SplitMatchProbability

Probability of matching this well

Identify and remove trivial splits

Convert object to Splits

Generate trivial trees

Extract a subtree

TreesMatchingTree

Number of trees containing a tree

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Brewer palettes

Random parent vector

TreesMatchingSplit

Number of trees matching a bipartition split

Root or unroot a phylogenetic tree

Select element at random

Exclusive OR operation

Unique integer indices for bifurcating tree topologies

Add tree to start of list

Is tree rooted?

doubleFactorials

Double factorials

sort.multiPhylo

Sort a list of phylogenetic trees

Efficiently convert edge matrix to splits

WriteTntCharacters

Write morphological character matrix to TNT file

Is an object a TreeNumber object?

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

logDoubleFactorials

Natural logarithms of double factorials

Extract tip labels

Colour for node support value

"Stemwardness" of a leaf

UnrootedTreesMatchingSplit

Number of trees consistent with split

Remove metadata from trees

Remove quotation marks from a string

TotalCopheneticIndex

Total Cophenetic Index

Integer representing shape of a tree

Write a phylogenetic tree in Newick format

TreeTools-package

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

Convert object to multiPhylo class

Wrapper for internal C function root_on_node()

match,phylo,phylo-method

match,Splits,Splits-method

ArtificialExtinction

Artificial Extinction

Read modification time from "ape" Nexus file

Collapse nodes on a phylogenetic tree

Convert phylogenetic tree to ClusterTable

ClusterTable-methods

S3 methods for ClusterTable objects

Cladistic information content of a tree

CharacterInformation

Character information content

Add a tip to a phylogenetic tree