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TreeTools (version 1.7.2)

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; tree rearrangement; analysis of tree shape; rooting of trees and extraction of subtrees; calculation and depiction of split support; plotting the position of rogue taxa (Klopfstein & Spasojevic 2019) ; calculation of ancestor-descendant relationships, of 'stemwardness' (Asher & Smith, 2021) , and of tree balance (Mir et al. 2013) ; artificial extinction (Asher & Smith, 2022) ; 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

1,996

Version

1.7.2

License

GPL (>= 3)

Issues

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Repository

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

Homepage

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

Maintainer

Martin R. Smith

Last Published

May 24th, 2022

Functions in TreeTools (1.7.2)

Read modification time from 'ape' Nexus file

Collapse nodes on a phylogenetic tree

Add a tip to a phylogenetic tree

Cladistic information content of a tree

DescendantEdges

Identify descendant edges

DoubleFactorial

Double factorial

EnforceOutgroup

Generate a tree with a specified outgroup

Distance between edges

ClusterTable-methods

S3 methods for ClusterTable objects

Add full stop to end of a sentence

NonDuplicateRoot

Non-duplicate root

Paths present in reduced tree

ImposeConstraint

Force a tree to match a constraint

Order of each node in a tree

CharacterInformation

Character information content

CompatibleSplits

Which splits are compatible?

Convert between strings and phyDat objects

Constrained neighbour-joining tree

ConsensusWithout

Reduced consensus, omitting specified taxa

Minimum spanning tree

Polarize splits on a single taxon

Extract taxa from a matrix block

LeafLabelInterchange

Leaf label interchange

Convert between matrices and phyDat objects

Number of trees

MorphoBankDecode

Decode MorphoBank text

Generate a neighbour joining tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of distinct splits

Construct consensus trees

Identify vertices retained when leaves are dropped

Data from Zhang et al. 2016

Most recent common ancestor

Tips contained within splits

Extract tip labels

Reorder tree edges and nodes

Generate pectinate, balanced or random trees

Generate binary tree by collapsing polytomies

logDoubleFactorials

Natural logarithms of double factorials

Visualize position of rogue taxa

Number of leaves in a phylogenetic tree

Which node is a tree's root?

Write Newick Tree

Hamming distance between taxa in a phylogenetic dataset

Number of trees one SPR step away

RightmostCharacter

Rightmost character of string

SingleTaxonTree

Generate a single taxon tree

SplitMatchProbability

Probability of matching this well

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Is tree rooted?

TreesMatchingSplit

Number of trees matching a bipartition split

TreeTools-package

TotalCopheneticIndex

Total Cophenetic Index

Count descendants for each node in a tree

Reorder edges of a phylogenetic tree

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

Calculate length of paths between each pair of vertices within tree

Renumber a tree's tips

Renumber a tree's nodes and tips

PairwiseDistances

Distances between each pair of trees

Read phylogenetic characters from file

Distance of each node from tree exterior

Unique integer indices for bifurcating tree topologies

Integer representing shape of a tree

Root or unroot a phylogenetic tree

Extract a subtree

Add tree to start of list

Colour for node support value

Convert object to Splits

SplitsInBinaryTree

Maximum splits in an n-leaf tree

doubleFactorials

Double factorials

WriteTntCharacters

Write morphological character matrix to TNT file

Write a phylogenetic tree in Newick format

Convert object to multiPhylo class

UnrootedTreesMatchingSplit

Number of trees consistent with split

Remove quotation marks from a string

Efficiently convert edge matrix to splits

Brewer palettes

Exclusive OR operation

Random parent vector

'Stemwardness' of a leaf

Produce a legend for continuous gradient scales

Frequency of splits

Subset of a split on fewer leaves

Identify and remove trivial splits

sort.multiPhylo

Sort a list of phylogenetic trees

TreesMatchingTree

Number of trees containing a tree

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

ArtificialExtinction

Artificial Extinction

Convert phylogenetic tree to ClusterTable

Drop leaves from tree

Ancestors of an edge