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TreeTools (version 0.1.2)

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

0.1.2

License

GPL (>= 3)

Issues

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Maintainer

Martin R. Smith

Last Published

December 18th, 2019

Functions in TreeTools (0.1.2)

ConsensusWithout

Consensus without taxa
NTip

Number of tips in a phylogenetic tree
ReadTntTree

Parse TNT Tree
EdgeDistances

Distance between edges
NSplits

Number of distinct partitions
SingleTaxonTree

SingleTaxonTree
EdgeAncestry

Edge ancestry
ReadCharacters

Read characters from Nexus file
SortTree

Sort tree
AllAncestors

List all ancestral nodes
TreeNumber

Unique integer indices for bifurcating tree topologies
EnforceOutgroup

Force taxa to form an outgroup
.DecodeRaw

Decode Splits objects
DescendantEdges

Descendant Edges
DoubleFactorial

Double Factorial
MRCA

Most Recent Common Ancestor
ExtractTaxa

Extract taxa from a matrix block
in.Splits

Splits in Splits object
TreeShape

Integer representing shape of a tree
doubleFactorials

Double factorials
NJTree

Neighbour Joining Tree
N1Spr

Number of trees one SPR step away
NonDuplicateRoot

Non-duplicate root
Lobo.data

Raw data from Zhang et al. 2016
Lobo.phy

Data from Zhang et al. 2016 in phyDat format
NewickTree

Newick Tree
Subsplit

Subset of a split on fewer taxa
RenumberTips

Renumber a tree's tips
PectinateTree

Generate a Pectinate Tree
NPartitionPairs

Distributions of tips consistent with a partition pair
Renumber

Renumber a tree's nodes and tips
TreeTools-package

TreeTools: Create, Modify and Analyse Phylogenetic Trees
MatrixToPhyDat

Matrix to phyDat
NRooted

Number of rooted/unrooted trees
Subtree

Extract subtree
TreesMatchingSplit

Number of trees matching a bipartition split
as.Splits

As splits
Neworder

Reorder edges of a phylogenetic tree
PhyToString

phyDat to String
brewer

Brewer palettes
print.TreeNumber

Print TreeNumber object
TipLabels

Extract tip labels
RootTree

Root a phylogenetic tree
SupportColour

Support colour
RightmostCharacter

Rightmost character of string
RandomTree

Generate a random tree topology
SplitMatchProbability

Probability of matching this well
SampleOne

Quick sample
RenumberTree

Renumber a tree in preorder
SplitFrequency

Frequency of splits
StringToPhyDat

String to phyDat
SplitInformation

Information content of a split
match.Splits

Match splits
UnrootedTreesMatchingSplit

Number of trees consistent with split
logDoubleFactorials

Natural logarithms of double factorials
TrivialSplits

Are splits trivial?
TipsInSplits

Tips contained within splits
UnshiftTree

Add Tree to Start of List
as.Newick

Write a phylogenetic tree in Newick format
TreeIsRooted

Is tree rooted?
AddTip

Add a tip to a phylogenetic tree
BalancedTree

Generate a Balanced Tree
AncestorEdge

Ancestral edge
ApeTime

Ape Time
CollapseNode

Collapse nodes on a phylogenetic tree
CharacterInformation

Character information content
CompatibleSplits

Which splits are compatible?
Cladewise

Reorder trees
CladeSizes

Clade sizes