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TreeTools (version 1.10.0)

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; 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, 2022) , 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

1.10.0

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

August 19th, 2023

Functions in TreeTools (1.10.0)

Add full stop to end of a sentence

Drop leaves from tree

LeafLabelInterchange

Leaf label interchange

Constrained neighbour-joining tree

ConsensusWithout

Reduced consensus, omitting specified taxa

ImposeConstraint

Force a tree to match a constraint

Paths present in reduced tree

Construct consensus trees

Generate pectinate, balanced or random trees

CompatibleSplits

Which splits are compatible?

EnforceOutgroup

Generate a tree with a specified outgroup

Extract taxa from a matrix block

Number of leaves in a phylogenetic tree

Most recent common ancestor

Hamming distance between taxa in a phylogenetic dataset

Write Newick Tree

Data from Zhang et al. 2016

Ancestors of an edge

DescendantEdges

Identify descendant edges

DoubleFactorial

Double factorial

Minimum spanning tree

Generate binary tree by collapsing polytomies

Convert between matrices and phyDat objects

MorphoBankDecode

Decode MorphoBank text

Renumber a tree's nodes and tips

Identify vertices retained when leaves are dropped

Number of trees one SPR step away

Reorder edges of a phylogenetic tree

Reorder tree edges and nodes

Number of trees

RightmostCharacter

Rightmost character of string

Distance of each node from tree exterior

Count descendants for each node in a tree

Number of distinct splits

Visualize position of rogue taxa

Which node is a tree's root?

Unique integer indices for bifurcating tree topologies

Renumber a tree's tips

Frequency of splits

Root or unroot a phylogenetic tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Generate a neighbour joining tree

TotalCopheneticIndex

Total Cophenetic Index

Produce a legend for continuous gradient scales

Write a phylogenetic tree in Newick format

WriteTntCharacters

Write morphological character matrix to TNT file

Is tree rooted?

Polarize splits on a single taxon

PairwiseDistances

Distances between each pair of trees

SplitsInBinaryTree

Maximum splits in an n-leaf tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Number of edges incident to each node in a tree

Convert between strings and phyDat objects

Display time-calibrated tree using tip information only

Read phylogenetic characters from file

"Stemwardness" of a leaf

Calculate length of paths between each pair of vertices within tree

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Tips contained within splits

TreesMatchingTree

Number of trees containing a tree

Integer representing shape of a tree

SplitMatchProbability

Probability of matching this well

Identify and remove trivial splits

Convert object to multiPhylo class

Number of rooted / unrooted tree shapes

Extract tip labels

Convert object to Splits

Colour for node support value

print.TreeNumber

Print TreeNumber object

UnrootedTreesMatchingSplit

Number of trees consistent with split

Add tree to start of list

doubleFactorials

Double factorials

Remove quotation marks from a string

Random parent vector

Generate trivial trees

sort.multiPhylo

Sort a list of phylogenetic trees

Exclusive OR operation

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

Brewer palettes

logDoubleFactorials

Natural logarithms of double factorials

Is an object a TreeNumber object?

TreesMatchingSplit

Number of trees matching a bipartition split

Efficiently convert edge matrix to splits

TreeTools-package

Subset of a split on fewer leaves

Extract a subtree

Cladistic information content of a tree

Read modification time from "ape" Nexus file

Collapse nodes on a phylogenetic tree

CharacterInformation

Character information content

Convert phylogenetic tree to ClusterTable

ArtificialExtinction

Artificial Extinction

Add a tip to a phylogenetic tree

ClusterTable-methods

S3 methods for ClusterTable objects

Distance between edges