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TreeTools (version 1.3.0)

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; 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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Version

Install

install.packages('TreeTools')

Monthly Downloads

1,855

Version

1.3.0

License

GPL (>= 3)

Issues

Pull Requests

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Forks

Repository

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

Homepage

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

Maintainer

Martin R. Smith

Last Published

September 22nd, 2020

Functions in TreeTools (1.3.0)

Add a tip to a phylogenetic tree

EnforceOutgroup

Generate a tree with a specific outgroup

Number of trees one SPR step away

Count descendants for each node in a tree

Distance of each node from tree exterior

Reorder edges of a phylogenetic tree

Read modification time from 'ape' Nexus file

'Stemwardness' of a leaf

Root or unroot a phylogenetic tree

ArtificialExtinction

Artificial Extinction

Subset of a split on fewer leaves

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

DescendantEdges

Identify descendant edges

DoubleFactorial

Double factorial

Write Newick Tree

Number of leaves in a phylogenetic tree

Data from Zhang et al. 2016

RightmostCharacter

Rightmost character of string

CharacterInformation

Character information content

Extract a subtree

Which node is a tree's root?

Colour for node support value

TreeTools-package

TreesMatchingSplit

Number of trees matching a bipartition split

Random parent vector

doubleFactorials

Double factorials

logDoubleFactorials

Natural logarithms of double factorials

LeafLabelInterchange

Leaf label interchange

Generate a neighbour joining tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Order of each node in a tree

Renumber a tree's tips

NonDuplicateRoot

Non-duplicate root

Frequency of splits

Drop tips from tree

Cladistic information content of a tree

Collapse nodes on a phylogenetic tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

UnrootedTreesMatchingSplit

Number of trees consistent with split

Convert object to Splits

Add tree to start of list

Brewer palettes

CompatibleSplits

Which splits are compatible?

Most recent common ancestor

Ancestors of an edge

Edges of minimum spanning tree

Number of distinct splits

Number of trees

ConsensusWithout

Consensus without taxa

Renumber a tree's nodes and tips

Extract taxa from a matrix block

Generate pectinate, balanced or random trees

SplitMatchProbability

Probability of matching this well

SplitsInBinaryTree

Maximum splits in an n-leaf tree

TreesMatchingTree

Number of trees containing a tree

Generate binary tree by collapsing polytomies

Convert between matrices and phyDat objects

Convert between strings and phyDat objects

Read phylogenetic characters from file

Identify and remove trivial splits

WriteTntCharacters

Write morphological character matrix to TNT file

SingleTaxonTree

Generate a single taxon tree

Extract tip labels

Tips contained within splits

Write a phylogenetic tree in Newick format

Is tree rooted?

TotalCopheneticIndex

Total Cophenetic Index

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

Number of rooted / unrooted tree shapes

print.TreeNumber

Print TreeNumber object

Distance between edges