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TreeTools (version 0.1.4)

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 partition information.

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Install

install.packages('TreeTools')

Monthly Downloads

1,738

Version

0.1.4

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

March 4th, 2020

Functions in TreeTools (0.1.4)

ConsensusWithout

Consensus without taxa

Generate a Balanced Tree

Collapse nodes on a phylogenetic tree

CharacterInformation

Character information content

List all ancestral nodes

Add a tip to a phylogenetic tree

Tips contained within splits

Extract taxa from a matrix block

CompatibleSplits

Which splits are compatible?

Distance between edges

EnforceOutgroup

Force taxa to form an outgroup

DescendantEdges

Descendant Edges

Renumber a tree's tips

Reorder edges of a phylogenetic tree

Decode Splits objects

Data from Zhang et al. 2016 in phyDat format

print.TreeNumber

Print TreeNumber object

Renumber a tree's nodes and tips

Raw data from Zhang et al. 2016

Most Recent Common Ancestor

Number of rooted/unrooted trees

Number of tips in a phylogenetic tree

Matrix to phyDat

DoubleFactorial

Double Factorial

Number of distinct partitions

TreesMatchingSplit

Number of trees matching a bipartition split

Number of trees one SPR step away

Frequency of splits

Neighbour Joining Tree

NPartitionPairs

Distributions of tips consistent with a partition pair

Generate a random tree topology

Are splits trivial?

Subset of a split on fewer taxa

NonDuplicateRoot

Non-duplicate root

Generate a Pectinate Tree

SplitMatchProbability

Probability of matching this well

Read characters from Nexus file

logDoubleFactorials

Natural logarithms of double factorials

Unique integer indices for bifurcating tree topologies

SplitInformation

Information content of a split

Root a phylogenetic tree

UnrootedTreesMatchingSplit

Number of trees consistent with split

Add Tree to Start of List

Write a phylogenetic tree in Newick format

Integer representing shape of a tree

RightmostCharacter

Rightmost character of string

Extract subtree

TreeTools-package

'TreeTools' is an R package that provides functions for creating, modifying and analysing phylogenetic trees. It complements packages such as 'ape', 'phangorn' and 'phytools', aiming for efficient and robust implementations of functions, typically applied to unweighted trees (i.e. those without edge lengths).

String to phyDat

phyDat to String

Extract tip labels

doubleFactorials

Double factorials

Splits in Splits object

SingleTaxonTree

Single Taxon Tree

Is tree rooted?

Renumber a tree in preorder

Brewer palettes