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TreeTools (version 1.13.0)

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

1,498

Version

1.13.0

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

January 10th, 2025

Functions in TreeTools (1.13.0)

Ancestors of an edge

ConsensusWithout

Reduced consensus, omitting specified taxa

DescendantEdges

Identify descendant edges

Constrained neighbour-joining tree

Distance between edges

Decompose additive (ordered) phylogenetic characters

DoubleFactorial

Double factorial

Construct consensus trees

CompatibleSplits

Which splits are compatible?

Drop leaves from tree

Hamming distance between taxa in a phylogenetic dataset

Extract taxa from a matrix block

EnforceOutgroup

Generate a tree with a specified outgroup

Identify vertices retained when leaves are dropped

Add full stop to end of a sentence

Generate pectinate, balanced or random trees

Robust universal tree balance index

Minimum spanning tree

Most recent common ancestor

Data from Zhang et al. 2016

Convert between matrices and phyDat objects

Match nodes and edges between trees

Generate a neighbour joining tree

Generate binary tree by collapsing polytomies

Count descendants for each node in a tree

LeafLabelInterchange

Leaf label interchange

Write Newick Tree

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

ImposeConstraint

Force a tree to match a constraint

Reorder edges of a phylogenetic tree

Renumber a tree's nodes and tips

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

Renumber a tree's tips

Number of distinct splits

Number of leaves in a phylogenetic tree

Number of trees one SPR step away

Paths present in reduced tree

MorphoBankDecode

Decode MorphoBank text

NPartitionPairs

Distributions of tips consistent with a partition pair

PairwiseDistances

Distances between each pair of trees

Number of trees

Number of edges incident to each node in a tree

Convert between strings and phyDat objects

Calculate length of paths between each pair of vertices within tree

Visualize position of rogue taxa

Root or unroot a phylogenetic tree

Polarize splits on a single taxon

Read phylogenetic characters from file

Reorder tree edges and nodes

RightmostCharacter

Rightmost character of string

Frequency of splits

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

SplitMatchProbability

Probability of matching this well

Colour for node support value

Extract tip labels

Select element at random

Produce a legend for continuous gradient scales

Which node is a tree's root?

SplitsInBinaryTree

Maximum splits in an n-leaf tree

"Stemwardness" of a leaf

Convert object to Splits

Integer representing shape of a tree

Subset of a split on fewer leaves

Extract a subtree

TreeTools-package

Display time-calibrated tree using tip information only

Tips contained within splits

Is tree rooted?

Unique integer indices for bifurcating tree topologies

Efficiently convert edge matrix to splits

Identify and remove trivial splits

Remove metadata from trees

TotalCopheneticIndex

Total Cophenetic Index

Generate trivial trees

TreesMatchingSplit

Number of trees matching a bipartition split

TreesMatchingTree

Number of trees containing a tree

WriteTntCharacters

Write morphological character matrix to TNT file

Add tree to start of list

Random parent vector

Number of rooted / unrooted tree shapes

match,Splits,Splits-method

match,phylo,phylo-method

Brewer palettes

doubleFactorials

Double factorials

Is an object a TreeNumber object?

Write a phylogenetic tree in Newick format

logDoubleFactorials

Natural logarithms of double factorials

Remove quotation marks from a string

UnrootedTreesMatchingSplit

Number of trees consistent with split

sort.multiPhylo

Sort a list of phylogenetic trees

Exclusive OR operation

print.TreeNumber

Print TreeNumber object

Convert object to multiPhylo class

Wrapper for internal C function root_on_node()

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

Add a tip to a phylogenetic tree

ClusterTable-methods

S3 methods for ClusterTable objects

Cladistic information content of a tree

Read modification time from "ape" Nexus file

ArtificialExtinction

Artificial Extinction

Collapse nodes on a phylogenetic tree

Convert phylogenetic tree to ClusterTable

CharacterInformation

Character information content