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TreeTools (version 1.1.0)

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

1,996

Version

1.1.0

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

July 7th, 2020

Functions in TreeTools (1.1.0)

DescendantEdges

Identify descendant edges

CompatibleSplits

Which splits are compatible?

CharacterInformation

Character information content

Cladistic information content

ConsensusWithout

Consensus without taxa

Read modification time from 'ape' Nexus file

Collapse nodes on a phylogenetic tree

Add a tip to a phylogenetic tree

LeafLabelInterchange

Leaf label interchange

Distance of each node from tree exterior

Reorder edges of a phylogenetic tree

Generate pectinate, balanced or random trees

Most recent common ancestor

Ancestors of an edge

Distance between edges

Generate binary tree by collapsing polytomies

Data from Zhang et al. 2016

DoubleFactorial

Double factorial

Drop tips from tree

NonDuplicateRoot

Non-duplicate root

Count descendants for each node in a tree

SplitInformation

Phylogenetic information content of splitting leaves into two partitions

Number of trees one SPR step away

Order of each node in a tree

Frequency of splits

Is tree rooted?

EnforceOutgroup

Generate a tree with a specific outgroup

Extract taxa from a matrix block

Number of trees

Unique integer indices for bifurcating tree topologies

TreesMatchingTree

Number of trees containing a tree

TreesMatchingSplit

Number of trees matching a bipartition split

SingleTaxonTree

Generate a single taxon tree

Colour for node support value

Extract tip labels

Generate a neighbour joining tree

Number of leaves in a phylogenetic tree

Number of distinct splits

Random parent vector

Convert between matrices and phyDat objects

doubleFactorials

Double factorials

NPartitionPairs

Distributions of tips consistent with a partition pair

Subset of a split on fewer leaves

Which node is a tree's root?

Read phylogenetic characters from file

Convert between strings and phyDat objects

RightmostCharacter

Rightmost character of string

Root or unroot a phylogenetic tree

Renumber a tree's nodes and tips

Identify and remove trivial splits

Extract a subtree

Number of rooted / unrooted tree shapes

Write Newick Tree

Convert object to Splits

Brewer palettes

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

UnrootedTreesMatchingSplit

Number of trees consistent with split

Renumber a tree's tips

TotalCopheneticIndex

Total Cophenetic Index

Write a phylogenetic tree in Newick format

Add tree to start of list

Tips contained within splits

SplitMatchProbability

Probability of matching this well

print.TreeNumber

Print TreeNumber object

SplitsInBinaryTree

Maximum splits in an n-leaf tree

Integer representing shape of a tree

logDoubleFactorials

Natural logarithms of double factorials

TreeTools-package