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TreeTools (version 1.4.4)

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.

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Install

install.packages('TreeTools')

Monthly Downloads

1,855

Version

1.4.4

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

April 20th, 2021

Functions in TreeTools (1.4.4)

CompatibleSplits

Which splits are compatible?

Read modification time from 'ape' Nexus file

Cladistic information content of a tree

CharacterInformation

Character information content

ArtificialExtinction

Artificial Extinction

ConsensusWithout

Consensus without taxa

Collapse nodes on a phylogenetic tree

Add a tip to a phylogenetic tree

Drop tips from tree

DoubleFactorial

Double factorial

DescendantEdges

Identify descendant edges

Ancestors of an edge

EnforceOutgroup

Generate a tree with a specific outgroup

Distance between edges

LeafLabelInterchange

Leaf label interchange

Generate a neighbour joining tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Extract taxa from a matrix block

Number of trees

Generate binary tree by collapsing polytomies

Generate pectinate, balanced or random trees

Number of distinct splits

Convert between matrices and phyDat objects

Minimum spanning tree

Most recent common ancestor

Order of each node in a tree

Number of leaves in a phylogenetic tree

Data from Zhang et al. 2016

Convert between strings and phyDat objects

Which node is a tree's root?

Root or unroot a phylogenetic tree

Count descendants for each node in a tree

Reorder edges of a phylogenetic tree

Renumber a tree's nodes and tips

Number of trees one SPR step away

Renumber a tree's tips

Distance of each node from tree exterior

Read phylogenetic characters from file

Write Newick Tree

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Frequency of splits

Tips contained within splits

Colour for node support value

Extract tip labels

TreeTools-package

Integer representing shape of a tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

PairwiseDistances

Distances between each pair of trees

NonDuplicateRoot

Non-duplicate root

SingleTaxonTree

Generate a single taxon tree

Convert object to multiPhylo class

TotalCopheneticIndex

Total Cophenetic Index

Brewer palettes

Identify and remove trivial splits

Random parent vector

RightmostCharacter

Rightmost character of string

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

Number of rooted / unrooted tree shapes

Is tree rooted?

SplitMatchProbability

Probability of matching this well

UnrootedTreesMatchingSplit

Number of trees consistent with split

Add tree to start of list

Unique integer indices for bifurcating tree topologies

'Stemwardness' of a leaf

logDoubleFactorials

Natural logarithms of double factorials

TreesMatchingSplit

Number of trees matching a bipartition split

WriteTntCharacters

Write morphological character matrix to TNT file

Extract a subtree

Subset of a split on fewer leaves

print.TreeNumber

Print TreeNumber object

Convert object to Splits

Write a phylogenetic tree in Newick format

doubleFactorials

Double factorials

TreesMatchingTree

Number of trees containing a tree