Learn R Programming

⚠️There's a newer version (1.14.0) of this package.Take me there.

TreeTools (version 1.7.0)

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, 2021) , and of tree balance (Mir et al. 2013) ; 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.

Copy Link

Version

Install

install.packages('TreeTools')

Monthly Downloads

1,996

Version

1.7.0

License

GPL (>= 3)

Issues

Pull Requests

Stars

Forks

Repository

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

Homepage

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

Maintainer

Martin R. Smith

Last Published

March 21st, 2022

Functions in TreeTools (1.7.0)

Collapse nodes on a phylogenetic tree

CharacterInformation

Character information content

ArtificialExtinction

Artificial Extinction

Cladistic information content of a tree

Construct consensus trees

Read modification time from 'ape' Nexus file

Add a tip to a phylogenetic tree

CompatibleSplits

Which splits are compatible?

EnforceOutgroup

Generate a tree with a specified outgroup

Add full stop to end of a sentence

Distance between edges

ConsensusWithout

Reduced consensus, omitting specified taxa

Identify vertices retained when leaves are dropped

Constrained neighbour-joining tree

LeafLabelInterchange

Leaf label interchange

Extract taxa from a matrix block

Minimum spanning tree

Generate a neighbour joining tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Order of each node in a tree

Generate binary tree by collapsing polytomies

Number of leaves in a phylogenetic tree

Count descendants for each node in a tree

Number of trees one SPR step away

Write Newick Tree

Reorder edges of a phylogenetic tree

Generate pectinate, balanced or random trees

Hamming distance between taxa in a phylogenetic dataset

Calculate length of paths between each pair of vertices within tree

Distance of each node from tree exterior

NonDuplicateRoot

Non-duplicate root

Drop leaves from tree

Root or unroot a phylogenetic tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Reorder tree edges and nodes

SplitMatchProbability

Probability of matching this well

RightmostCharacter

Rightmost character of string

MorphoBankDecode

Decode MorphoBank text

PairwiseDistances

Distances between each pair of trees

Read phylogenetic characters from file

Convert between matrices and phyDat objects

Extract a subtree

Colour for node support value

Extract tip labels

Tips contained within splits

ImposeConstraint

Force a tree to match a constraint

Ancestors of an edge

Number of trees

Paths present in reduced tree

Convert object to Splits

Unique integer indices for bifurcating tree topologies

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Exclusive OR operation

Write a phylogenetic tree in Newick format

Random parent vector

DescendantEdges

Identify descendant edges

DoubleFactorial

Double factorial

Convert between strings and phyDat objects

Brewer palettes

Remove quotation marks from a string

UnrootedTreesMatchingSplit

Number of trees consistent with split

Polarize splits on a single taxon

Integer representing shape of a tree

Convert object to multiPhylo class

Data from Zhang et al. 2016

Number of distinct splits

sort.multiPhylo

Sort a list of phylogenetic trees

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

Is tree rooted?

TotalCopheneticIndex

Total Cophenetic Index

Which node is a tree's root?

doubleFactorials

Double factorials

Visualize position of rogue taxa

Subset of a split on fewer leaves

'Stemwardness' of a leaf

Efficiently convert edge matrix to splits

Most recent common ancestor

TreeTools-package

Renumber a tree's tips

Add tree to start of list

SingleTaxonTree

Generate a single taxon tree

WriteTntCharacters

Write morphological character matrix to TNT file

Renumber a tree's nodes and tips

logDoubleFactorials

Natural logarithms of double factorials

Produce a legend for continuous gradient scales

Frequency of splits

print.TreeNumber

Print TreeNumber object

TreesMatchingSplit

Number of trees matching a bipartition split

TreesMatchingTree

Number of trees containing a tree

Identify and remove trivial splits

Number of rooted / unrooted tree shapes