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TreeTools (version 1.0.0)

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 partitions and cladistic information.

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Version

Install

install.packages('TreeTools')

Monthly Downloads

1,384

Version

1.0.0

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

June 8th, 2020

Functions in TreeTools (1.0.0)

EnforceOutgroup

Generate a tree with a specific outgroup

DoubleFactorial

Double factorial

Order of each node in a tree

Distance between edges

Generate a neighbour joining tree

SplitMatchProbability

Probability of matching this well

Count descendants for each node in a tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Ancestors of an edge

Distance of each node from tree exterior

Subset of a split on fewer leaves

Drop tips from tree

NonDuplicateRoot

Non-duplicate root

Convert between strings and phyDat objects

Is tree rooted?

Number of trees one SPR step away

Convert between matrices and phyDat objects

Unique integer indices for bifurcating tree topologies

Number of distinct splits

Extract taxa from a matrix block

SingleTaxonTree

Generate a single taxon tree

TreeTools-package

Add tree to start of list

Number of leaves in a phylogenetic tree

DescendantEdges

Identify descendant edges

Integer representing shape of a tree

Generate pectinate, balanced or random trees

Write a phylogenetic tree in Newick format

Renumber a tree's nodes and tips

TreesMatchingTree

Number of trees containing a tree

TreesMatchingSplit

Number of trees matching a bipartition split

Extract a subtree

Number of rooted / unrooted tree shapes

LeafLabelInterchange

Leaf label interchange

Renumber a tree's tips

Number of trees

Frequency of splits

Reorder edges of a phylogenetic tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Convert object to Splits

Tips contained within splits

TotalCopheneticIndex

Total Cophenetic Index

Write Newick Tree

Data from Zhang et al. 2016

Most recent common ancestor

Brewer palettes

Which node is a tree's root?

Read phylogenetic characters from file

Identify and remove trivial splits

Colour for node support value

Root or unroot a phylogenetic tree

UnrootedTreesMatchingSplit

Number of trees consistent with split

Extract tip labels

print.TreeNumber

Print TreeNumber object

doubleFactorials

Double factorials

RightmostCharacter

Rightmost character of string

logDoubleFactorials

Natural logarithms of double factorials

CompatibleSplits

Which splits are compatible?

Collapse nodes on a phylogenetic tree

Cladistic information content

ConsensusWithout

Consensus without taxa

Add a tip to a phylogenetic tree

Read modification time from 'ape' Nexus file

CharacterInformation

Character information content