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TreeTools (version 0.1.3)

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

1,905

Version

0.1.3

License

GPL (>= 3)

Issues

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Maintainer

Martin R. Smith

Last Published

December 19th, 2019

Functions in TreeTools (0.1.3)

Lobo.data

Raw data from Zhang et al. 2016
AllAncestors

List all ancestral nodes
Cladewise

Reorder trees
Lobo.phy

Data from Zhang et al. 2016 in phyDat format
CharacterInformation

Character information content
AncestorEdge

Ancestral edge
ConsensusWithout

Consensus without taxa
BalancedTree

Generate a Balanced Tree
.DecodeRaw

Decode Splits objects
NewickTree

Newick Tree
DescendantEdges

Descendant Edges
Neworder

Reorder edges of a phylogenetic tree
CompatibleSplits

Which splits are compatible?
DoubleFactorial

Double Factorial
N1Spr

Number of trees one SPR step away
EdgeAncestry

Edge ancestry
NSplits

Number of distinct partitions
NTip

Number of tips in a phylogenetic tree
EdgeDistances

Distance between edges
SplitMatchProbability

Probability of matching this well
NonDuplicateRoot

Non-duplicate root
PectinateTree

Generate a Pectinate Tree
ReadCharacters

Read characters from Nexus file
ReadTntTree

Parse TNT Tree
NJTree

Neighbour Joining Tree
ApeTime

Ape Time
StringToPhyDat

String to phyDat
RightmostCharacter

Rightmost character of string
RenumberTree

Renumber a tree in preorder
Subsplit

Subset of a split on fewer taxa
UnrootedTreesMatchingSplit

Number of trees consistent with split
TrivialSplits

Are splits trivial?
MRCA

Most Recent Common Ancestor
ExtractTaxa

Extract taxa from a matrix block
SplitFrequency

Frequency of splits
EnforceOutgroup

Force taxa to form an outgroup
MatrixToPhyDat

Matrix to phyDat
RenumberTips

Renumber a tree's tips
SortTree

Sort tree
NPartitionPairs

Distributions of tips consistent with a partition pair
TipsInSplits

Tips contained within splits
Renumber

Renumber a tree's nodes and tips
SingleTaxonTree

SingleTaxonTree
as.Splits

As splits
TreeNumber

Unique integer indices for bifurcating tree topologies
SplitInformation

Information content of a split
TreeShape

Integer representing shape of a tree
TreeIsRooted

Is tree rooted?
logDoubleFactorials

Natural logarithms of double factorials
match.Splits

Match splits
doubleFactorials

Double factorials
in.Splits

Splits in Splits object
Subtree

Extract subtree
brewer

Brewer palettes
TreesMatchingSplit

Number of trees matching a bipartition split
as.Newick

Write a phylogenetic tree in Newick format
TreeTools-package

TreeTools: Create, Modify and Analyse Phylogenetic Trees
PhyToString

phyDat to String
UnshiftTree

Add Tree to Start of List
NRooted

Number of rooted/unrooted trees
RandomTree

Generate a random tree topology
SupportColour

Support colour
TipLabels

Extract tip labels
print.TreeNumber

Print TreeNumber object
RootTree

Root a phylogenetic tree
SampleOne

Quick sample
AddTip

Add a tip to a phylogenetic tree
CladeSizes

Clade sizes
CollapseNode

Collapse nodes on a phylogenetic tree