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TreeTools (version 1.4.2)

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; 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

1.4.2

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

January 26th, 2021

Functions in TreeTools (1.4.2)

Read modification time from 'ape' Nexus file

ArtificialExtinction

Artificial Extinction

LeafLabelInterchange

Leaf label interchange

Number of distinct splits

Number of trees

CharacterInformation

Character information content

Drop tips from tree

CompatibleSplits

Which splits are compatible?

ConsensusWithout

Consensus without taxa

Cladistic information content of a tree

Collapse nodes on a phylogenetic tree

Ancestors of an edge

Minimum spanning tree

DescendantEdges

Identify descendant edges

Most recent common ancestor

Distance between edges

DoubleFactorial

Double factorial

Read phylogenetic characters from file

Which node is a tree's root?

Data from Zhang et al. 2016

Number of leaves in a phylogenetic tree

Root or unroot a phylogenetic tree

Number of trees one SPR step away

Generate pectinate, balanced or random trees

Extract taxa from a matrix block

Write Newick Tree

Count descendants for each node in a tree

Subset of a split on fewer leaves

Extract a subtree

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Generate binary tree by collapsing polytomies

Convert between matrices and phyDat objects

'Stemwardness' of a leaf

Is tree rooted?

Brewer palettes

EnforceOutgroup

Generate a tree with a specific outgroup

Unique integer indices for bifurcating tree topologies

NPartitionPairs

Distributions of tips consistent with a partition pair

Generate a neighbour joining tree

PairwiseDistances

Distances between each pair of trees

Renumber a tree's tips

Renumber a tree's nodes and tips

Convert between strings and phyDat objects

Frequency of splits

Random parent vector

TreeTools-package

Reorder edges of a phylogenetic tree

Order of each node in a tree

Integer representing shape of a tree

NonDuplicateRoot

Non-duplicate root

Write a phylogenetic tree in Newick format

Convert object to Splits

SingleTaxonTree

Generate a single taxon tree

WriteTntCharacters

Write morphological character matrix to TNT file

Add tree to start of list

Distance of each node from tree exterior

Identify and remove trivial splits

RightmostCharacter

Rightmost character of string

UnrootedTreesMatchingSplit

Number of trees consistent with split

SplitMatchProbability

Probability of matching this well

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

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

TreesMatchingSplit

Number of trees matching a bipartition split

Colour for node support value

TreesMatchingTree

Number of trees containing a tree

doubleFactorials

Double factorials

Extract tip labels

Tips contained within splits

TotalCopheneticIndex

Total Cophenetic Index

logDoubleFactorials

Natural logarithms of double factorials

Add a tip to a phylogenetic tree