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TreeTools (version 1.12.0)

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, Lemant et al. 2022) , ; 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

1,345

Version

1.12.0

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

July 25th, 2024

Functions in TreeTools (1.12.0)

Ancestors of an edge

DoubleFactorial

Double factorial

Constrained neighbour-joining tree

Construct consensus trees

Drop leaves from tree

Distance between edges

Add full stop to end of a sentence

ImposeConstraint

Force a tree to match a constraint

Identify vertices retained when leaves are dropped

Paths present in reduced tree

Robust universal tree balance index

Data from Zhang et al. 2016

Convert between matrices and phyDat objects

MorphoBankDecode

Decode MorphoBank text

LeafLabelInterchange

Leaf label interchange

Match nodes and edges between trees

NPartitionPairs

Distributions of tips consistent with a partition pair

Number of trees one SPR step away

Count descendants for each node in a tree

Generate binary tree by collapsing polytomies

Generate a neighbour joining tree

Number of edges incident to each node in a tree

Numeric index of each node in a tree NodeNumbers() returns a sequence corresponding to the nodes in a tree

Distance of each node from tree exterior

Reorder edges of a phylogenetic tree

EnforceOutgroup

Generate a tree with a specified outgroup

Generate pectinate, balanced or random trees

Most recent common ancestor

Hamming distance between taxa in a phylogenetic dataset

Number of trees

Minimum spanning tree

Extract taxa from a matrix block

Number of distinct splits

Read phylogenetic characters from file

Renumber a tree's nodes and tips

Number of leaves in a phylogenetic tree

RightmostCharacter

Rightmost character of string

Polarize splits on a single taxon

Visualize position of rogue taxa

Convert between strings and phyDat objects

ReadMrBayesTrees

Read posterior tree sample produced by MrBayes

Calculate length of paths between each pair of vertices within tree

Which node is a tree's root?

Root or unroot a phylogenetic tree

PairwiseDistances

Distances between each pair of trees

Renumber a tree's tips

Reorder tree edges and nodes

Write Newick Tree

Extract a subtree

Colour for node support value

"Stemwardness" of a leaf

Subset of a split on fewer leaves

Produce a legend for continuous gradient scales

SplitMatchProbability

Probability of matching this well

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Convert object to Splits

SplitsInBinaryTree

Maximum splits in an n-leaf tree

TreeTools-package

TreesMatchingSplit

Number of trees matching a bipartition split

Tips contained within splits

Remove metadata from trees

TotalCopheneticIndex

Total Cophenetic Index

Frequency of splits

Unique integer indices for bifurcating tree topologies

Remove quotation marks from a string

Efficiently convert edge matrix to splits

Generate trivial trees

Is an object a TreeNumber object?

Brewer palettes

Convert object to multiPhylo class

Is tree rooted?

sort.multiPhylo

Sort a list of phylogenetic trees

WriteTntCharacters

Write morphological character matrix to TNT file

Exclusive OR operation

Integer representing shape of a tree

Write a phylogenetic tree in Newick format

TreesMatchingTree

Number of trees containing a tree

Identify and remove trivial splits

doubleFactorials

Double factorials

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

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

Wrapper for internal C function root_on_node()

Random parent vector

Add tree to start of list

Extract tip labels

Display time-calibrated tree using tip information only

UnrootedTreesMatchingSplit

Number of trees consistent with split

logDoubleFactorials

Natural logarithms of double factorials

Read modification time from "ape" Nexus file

CharacterInformation

Character information content

ClusterTable-methods

S3 methods for ClusterTable objects

Convert phylogenetic tree to ClusterTable

Collapse nodes on a phylogenetic tree

Cladistic information content of a tree

ArtificialExtinction

Artificial Extinction

Add a tip to a phylogenetic tree

ConsensusWithout

Reduced consensus, omitting specified taxa

CompatibleSplits

Which splits are compatible?

DescendantEdges

Identify descendant edges