# Create, Modify and Analyse Phylogenetic Trees

## Documentation for package ‘TreeTools’ version 0.1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F I L M N P R S T U W

## -- A --

AddTip | Add a tip to a phylogenetic tree
AddTipEverywhere | Add a tip to a phylogenetic tree
AllAncestors | List all ancestral nodes
AllDescendantEdges | Descendant Edges
ApeTime | Ape Time
as.logical.Splits | As splits
as.Newick | Write a phylogenetic tree in Newick format
as.Newick.list | Write a phylogenetic tree in Newick format
as.Newick.multiPhylo | Write a phylogenetic tree in Newick format
as.Newick.phylo | Write a phylogenetic tree in Newick format
as.phylo.numeric | Unique integer indices for bifurcating tree topologies
as.phylo.TreeNumber | Unique integer indices for bifurcating tree topologies
as.Splits | As splits
as.Splits.list | As splits
as.Splits.logical | As splits
as.Splits.multiPhylo | As splits
as.Splits.phylo | As splits
as.Splits.Splits | As splits
as.TreeNumber | Unique integer indices for bifurcating tree topologies
as.TreeNumber.character | Unique integer indices for bifurcating tree topologies
as.TreeNumber.multiPhylo | Unique integer indices for bifurcating tree topologies
as.TreeNumber.phylo | Unique integer indices for bifurcating tree topologies

## -- B --

BalancedTree | Generate a Balanced Tree
brewer | Brewer palettes

## -- C --

CharacterInformation | Character information content
CollapseEdge | Collapse nodes on a phylogenetic tree
CollapseNode | Collapse nodes on a phylogenetic tree
ConsensusWithout | Consensus without taxa

## -- D --

DescendantEdges | Descendant Edges
DoubleFactorial | Double Factorial
doubleFactorials | Double factorials

## -- E --

EdgeAncestry | Edge ancestry
EdgeDistances | Distance between edges
EnforceOutgroup | Force taxa to form an outgroup

## -- F --

ForestSplits | Frequency of splits

## -- I --

IC1Spr | Number of trees one SPR step away
in.Splits | Splits in Splits object

## -- L --

LnDoubleFactorial | Double Factorial
LnDoubleFactorial.int | Double Factorial
LnRooted | Number of rooted/unrooted trees
LnRooted.int | Number of rooted/unrooted trees
LnSplitMatchProbability | Probability of matching this well
LnTreesMatchingSplit | Number of trees matching a bipartition split
LnUnrooted | Number of rooted/unrooted trees
LnUnrooted.int | Number of rooted/unrooted trees
LnUnrootedMult | Number of rooted/unrooted trees
LnUnrootedSplits | Number of rooted/unrooted trees
Lobo.data | Raw data from Zhang et al. 2016
Lobo.phy | Data from Zhang et al. 2016 in 'phyDat' format
LogDoubleFactorial | Double Factorial
LogDoubleFactorial.int | Double Factorial
logDoubleFactorials | Natural logarithms of double factorials

## -- M --

MarkMissing | Consensus without taxa
match.Splits | Match splits
MRCA | Most Recent Common Ancestor
MultiSplitInformation | Information content of a split

## -- N --

N1Spr | Number of trees one SPR step away
NewickTree | Newick Tree
NJTree | Neighbour Joining Tree
NPartitionPairs | Distributions of tips consistent with a partition pair
NPartitions | Number of distinct partitions
NRooted | Number of rooted/unrooted trees
NSplits | Number of distinct partitions
NSplits.list | Number of distinct partitions
NSplits.multiPhylo | Number of distinct partitions
NSplits.numeric | Number of distinct partitions
NSplits.phylo | Number of distinct partitions
NSplits.Splits | Number of distinct partitions
NTip | Number of tips in a phylogenetic tree
NTip.list | Number of tips in a phylogenetic tree
NTip.multiPhylo | Number of tips in a phylogenetic tree
NTip.phylo | Number of tips in a phylogenetic tree
NTip.Splits | Number of tips in a phylogenetic tree
NUnrooted | Number of rooted/unrooted trees
NUnrootedMult | Number of rooted/unrooted trees
NUnrootedSplits | Number of rooted/unrooted trees

## -- P --

PectinateTree | Generate a Pectinate Tree
PhyDat | Read characters from Nexus file
PhyDatToString | 'phyDat' to String
PhydatToString | 'phyDat' to String
PhyToString | 'phyDat' to String
print.TreeNumber | Print 'TreeNumber' object

## -- R --

RandomTree | Generate a random tree topology
ReadAsPhyDat | Read characters from Nexus file
ReadCharacters | Read characters from Nexus file
ReadTntAsPhyDat | Read characters from Nexus file
ReadTntCharacters | Read characters from Nexus file
ReadTntTree | Parse TNT Tree
Renumber | Renumber a tree's nodes and tips
RenumberTips | Renumber a tree's tips
RenumberTips.list | Renumber a tree's tips
RenumberTips.multiPhylo | Renumber a tree's tips
RenumberTips.phylo | Renumber a tree's tips
RootOnNode | Root a phylogenetic tree
RootTree | Root a phylogenetic tree

## -- S --

SingleTaxonTree | Single Taxon Tree
SortTree | Sort tree
SplitFrequency | Frequency of splits
SplitInformation | Information content of a split
SplitMatchProbability | Probability of matching this well
SplitNumber | Frequency of splits
StringToPhyDat | String to 'phyDat'
StringToPhydat | String to 'phyDat'
Subsplit | Subset of a split on fewer taxa
Subtree | Extract subtree
SupportColor | Support colour
SupportColour | Support colour

## -- T --

TipLabels | Extract tip labels
TipLabels.character | Extract tip labels
TipLabels.default | Extract tip labels
TipLabels.list | Extract tip labels
TipLabels.matrix | Extract tip labels
TipLabels.multiPhylo | Extract tip labels
TipLabels.numeric | Extract tip labels
TipLabels.phyDat | Extract tip labels
TipLabels.phylo | Extract tip labels
TipLabels.Splits | Extract tip labels
TipLabels.TreeNumber | Extract tip labels
TipsInSplits | Tips contained within splits
TNTText2Tree | Parse TNT Tree
TreeIsRooted | Is tree rooted?
TreeNumber | Unique integer indices for bifurcating tree topologies
TreesMatchingSplit | Number of trees matching a bipartition split
TreeSplits | Frequency of splits
TrivialSplits | Are splits trivial?

## -- U --

UnrootedTreesMatchingSplit | Number of trees consistent with split
UnshiftTree | Add Tree to Start of List

## -- W --

WithoutTrivialSplits | Are splits trivial?