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TreeTools (version 1.2.0)

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; 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

1,738

Version

1.2.0

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 3rd, 2020

Functions in TreeTools (1.2.0)

Read modification time from 'ape' Nexus file

CharacterInformation

Character information content

Add a tip to a phylogenetic tree

ConsensusWithout

Consensus without taxa

ArtificialExtinction

Artificial Extinction

Cladistic information content of a tree

Collapse nodes on a phylogenetic tree

CompatibleSplits

Which splits are compatible?

Convert between strings and phyDat objects

Data from Zhang et al. 2016

LeafLabelInterchange

Leaf label interchange

DescendantEdges

Identify descendant edges

Drop tips from tree

SingleTaxonTree

Generate a single taxon tree

NonDuplicateRoot

Non-duplicate root

Distance between edges

Ancestors of an edge

NPartitionPairs

Distributions of tips consistent with a partition pair

EnforceOutgroup

Generate a tree with a specific outgroup

Number of trees

DoubleFactorial

Double factorial

Number of leaves in a phylogenetic tree

Number of distinct splits

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

SplitMatchProbability

Probability of matching this well

Extract taxa from a matrix block

Count descendants for each node in a tree

Read phylogenetic characters from file

TreeTools-package

TreesMatchingSplit

Number of trees matching a bipartition split

Generate a neighbour joining tree

Frequency of splits

RightmostCharacter

Rightmost character of string

Extract a subtree

logDoubleFactorials

Natural logarithms of double factorials

Identify and remove trivial splits

Order of each node in a tree

Generate pectinate, balanced or random trees

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

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Most recent common ancestor

Which node is a tree's root?

Generate binary tree by collapsing polytomies

Root or unroot a phylogenetic tree

TreesMatchingTree

Number of trees containing a tree

Subset of a split on fewer leaves

print.TreeNumber

Print TreeNumber object

Number of rooted / unrooted tree shapes

Write Newick Tree

Convert between matrices and phyDat objects

TotalCopheneticIndex

Total Cophenetic Index

Is tree rooted?

Extract tip labels

Number of trees one SPR step away

Reorder edges of a phylogenetic tree

Colour for node support value

Unique integer indices for bifurcating tree topologies

Distance of each node from tree exterior

Convert object to Splits

WriteTntCharacters

Write morphological character matrix to TNT file

Write a phylogenetic tree in Newick format

Brewer palettes

Renumber a tree's nodes and tips

Renumber a tree's tips

UnrootedTreesMatchingSplit

Number of trees consistent with split

Random parent vector

Tips contained within splits

Add tree to start of list

doubleFactorials

Double factorials

Integer representing shape of a tree