Learn R Programming

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

TreeTools (version 1.3.1)

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; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of node support; calculation of ancestor-descendant relationships; 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

1.3.1

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

October 3rd, 2020

Functions in TreeTools (1.3.1)

Read modification time from 'ape' Nexus file

Ancestors of an edge

ArtificialExtinction

Artificial Extinction

Drop tips from tree

ConsensusWithout

Consensus without taxa

DoubleFactorial

Double factorial

DescendantEdges

Identify descendant edges

CompatibleSplits

Which splits are compatible?

LeafLabelInterchange

Leaf label interchange

Generate a neighbour joining tree

Data from Zhang et al. 2016

Extract taxa from a matrix block

Distance between edges

Number of trees one SPR step away

Number of leaves in a phylogenetic tree

Count descendants for each node in a tree

EnforceOutgroup

Generate a tree with a specific outgroup

Edges of minimum spanning tree

Read phylogenetic characters from file

Convert between strings and phyDat objects

Most recent common ancestor

Root or unroot a phylogenetic tree

SingleTaxonTree

Generate a single taxon tree

Order of each node in a tree

Generate pectinate, balanced or random trees

Generate binary tree by collapsing polytomies

Convert between matrices and phyDat objects

Number of trees

NPartitionPairs

Distributions of tips consistent with a partition pair

Frequency of splits

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

NonDuplicateRoot

Non-duplicate root

Write Newick Tree

Number of distinct splits

Renumber a tree's nodes and tips

SplitMatchProbability

Probability of matching this well

SplitsInBinaryTree

Maximum splits in an n-leaf tree

TotalCopheneticIndex

Total Cophenetic Index

Reorder edges of a phylogenetic tree

Is tree rooted?

Random parent vector

Unique integer indices for bifurcating tree topologies

Convert object to Splits

Integer representing shape of a tree

Renumber a tree's tips

'Stemwardness' of a leaf

Subset of a split on fewer leaves

TreesMatchingSplit

Number of trees matching a bipartition split

TreeTools-package

Brewer palettes

Distance of each node from tree exterior

doubleFactorials

Double factorials

Extract tip labels

WriteTntCharacters

Write morphological character matrix to TNT file

Extract a subtree

Which node is a tree's root?

Write a phylogenetic tree in Newick format

RightmostCharacter

Rightmost character of string

Tips contained within splits

Colour for node support value

UnrootedTreesMatchingSplit

Number of trees consistent with split

Add tree to start of list

logDoubleFactorials

Natural logarithms of double factorials

TreesMatchingTree

Number of trees containing a tree

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

Number of rooted / unrooted tree shapes

print.TreeNumber

Print TreeNumber object

Identify and remove trivial splits

Add a tip to a phylogenetic tree

CharacterInformation

Character information content

Cladistic information content of a tree

Collapse nodes on a phylogenetic tree