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TreeTools (version 1.4.0)

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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Install

install.packages('TreeTools')

Monthly Downloads

1,512

Version

1.4.0

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

October 19th, 2020

Functions in TreeTools (1.4.0)

CompatibleSplits

Which splits are compatible?

Read modification time from 'ape' Nexus file

Cladistic information content of a tree

ConsensusWithout

Consensus without taxa

CharacterInformation

Character information content

ArtificialExtinction

Artificial Extinction

Add a tip to a phylogenetic tree

Collapse nodes on a phylogenetic tree

Distance between edges

NPartitionPairs

Distributions of tips consistent with a partition pair

Generate pectinate, balanced or random trees

Extract taxa from a matrix block

Generate a neighbour joining tree

Data from Zhang et al. 2016

LeafLabelInterchange

Leaf label interchange

Most recent common ancestor

Minimum spanning tree

EnforceOutgroup

Generate a tree with a specific outgroup

Distance of each node from tree exterior

Reorder edges of a phylogenetic tree

Generate binary tree by collapsing polytomies

DoubleFactorial

Double factorial

DescendantEdges

Identify descendant edges

Convert between matrices and phyDat objects

Number of trees

Count descendants for each node in a tree

Number of trees one SPR step away

Number of leaves in a phylogenetic tree

Drop tips from tree

Read phylogenetic characters from file

PairwiseDistances

Distances between each pair of trees

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

SplitMatchProbability

Probability of matching this well

Ancestors of an edge

Renumber a tree's tips

'Stemwardness' of a leaf

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Renumber a tree's nodes and tips

Convert between strings and phyDat objects

Tips contained within splits

SingleTaxonTree

Generate a single taxon tree

Number of distinct splits

doubleFactorials

Double factorials

Subset of a split on fewer leaves

TreesMatchingSplit

Number of trees matching a bipartition split

Brewer palettes

TreesMatchingTree

Number of trees containing a tree

Extract a subtree

Write Newick Tree

Root or unroot a phylogenetic tree

Colour for node support value

Which node is a tree's root?

Extract tip labels

TotalCopheneticIndex

Total Cophenetic Index

Frequency of splits

Random parent vector

UnrootedTreesMatchingSplit

Number of trees consistent with split

Convert object to Splits

Write a phylogenetic tree in Newick format

Identify and remove trivial splits

RightmostCharacter

Rightmost character of string

Is tree rooted?

Order of each node in a tree

NonDuplicateRoot

Non-duplicate root

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

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

WriteTntCharacters

Write morphological character matrix to TNT file

Add tree to start of list

logDoubleFactorials

Natural logarithms of double factorials

TreeTools-package