Learn R Programming

⚠️There's a newer version (1.13.1) of this package.Take me there.

TreeTools (version 1.9.2)

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) ; 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

1,384

Version

1.9.2

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

April 27th, 2023

Functions in TreeTools (1.9.2)

Distance between edges

Drop leaves from tree

ConsensusWithout

Reduced consensus, omitting specified taxa

CompatibleSplits

Which splits are compatible?

DescendantEdges

Identify descendant edges

Construct consensus trees

Constrained neighbour-joining tree

Ancestors of an edge

Add full stop to end of a sentence

DoubleFactorial

Double factorial

Paths present in reduced tree

EnforceOutgroup

Generate a tree with a specified outgroup

ImposeConstraint

Force a tree to match a constraint

Identify vertices retained when leaves are dropped

Hamming distance between taxa in a phylogenetic dataset

Generate pectinate, balanced or random trees

Extract taxa from a matrix block

LeafLabelInterchange

Leaf label interchange

Number of trees one SPR step away

Generate binary tree by collapsing polytomies

Minimum spanning tree

Generate a neighbour joining tree

Most recent common ancestor

Data from Zhang et al. 2016

Count descendants for each node in a tree

MorphoBankDecode

Decode MorphoBank text

Number of distinct splits

Write Newick Tree

Convert between matrices and phyDat objects

Number of trees

Number of leaves in a phylogenetic tree

Reorder edges of a phylogenetic tree

Distance of each node from tree exterior

Order of each node in a tree

NonDuplicateRoot

Non-duplicate root

Calculate length of paths between each pair of vertices within tree

PairwiseDistances

Distances between each pair of trees

NPartitionPairs

Distributions of tips consistent with a partition pair

Renumber a tree's nodes and tips

Renumber a tree's tips

Read phylogenetic characters from file

Convert between strings and phyDat objects

Polarize splits on a single taxon

SplitMatchProbability

Probability of matching this well

Root or unroot a phylogenetic tree

Convert object to Splits

Frequency of splits

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Reorder tree edges and nodes

RightmostCharacter

Rightmost character of string

Produce a legend for continuous gradient scales

Visualize position of rogue taxa

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Which node is a tree's root?

Is tree rooted?

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

TreeTools-package

TotalCopheneticIndex

Total Cophenetic Index

Convert object to multiPhylo class

Tips contained within splits

Write a phylogenetic tree in Newick format

Identify and remove trivial splits

doubleFactorials

Double factorials

Colour for node support value

logDoubleFactorials

Natural logarithms of double factorials

Extract tip labels

"Stemwardness" of a leaf

Generate trivial trees

Subset of a split on fewer leaves

Extract a subtree

sort.multiPhylo

Sort a list of phylogenetic trees

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

Efficiently convert edge matrix to splits

Exclusive OR operation

Random parent vector

Remove quotation marks from a string

UnrootedTreesMatchingSplit

Number of trees consistent with split

TreesMatchingTree

Number of trees containing a tree

Brewer palettes

TreesMatchingSplit

Number of trees matching a bipartition split

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

Add tree to start of list

WriteTntCharacters

Write morphological character matrix to TNT file

Add a tip to a phylogenetic tree

CharacterInformation

Character information content

Read modification time from "ape" Nexus file

ClusterTable-methods

S3 methods for ClusterTable objects

Collapse nodes on a phylogenetic tree

Convert phylogenetic tree to ClusterTable

ArtificialExtinction

Artificial Extinction

Cladistic information content of a tree