AddTip                  Add a tip to a phylogenetic tree
ApeTime                 Read modification time from 'ape' Nexus file
ArtificialExtinction    Artificial Extinction
CharacterInformation    Character information content
CladeSizes              Clade sizes
CladisticInfo           Cladistic information content of a tree
CollapseNode            Collapse nodes on a phylogenetic tree
Consensus               Consensus trees
ConsensusWithout        Reduced consensus, omitting specified taxa
ConstrainedNJ           Constrained neighbour-joining tree
DescendantEdges         Identify descendant edges
DoubleFactorial         Double factorial
DropTip                 Drop tips from tree
EdgeAncestry            Ancestors of an edge
EdgeDistances           Distance between edges
EndSentence             Add full stop to end of a sentence
EnforceOutgroup         Generate a tree with a specific outgroup
GenerateTree            Generate pectinate, balanced or random trees
ImposeConstraint        Force a tree to match a constraint
LabelSplits             Label splits
LeafLabelInterchange    Leaf label interchange
ListAncestors           List ancestors
Lobo.data               Data from Zhang et al. 2016
MRCA                    Most recent common ancestor
MSTEdges                Minimum spanning tree
MakeTreeBinary          Generate binary tree by collapsing polytomies
MorphoBankDecode        Decode MorphoBank text
N1Spr                   Number of trees one SPR step away
NDescendants            Count descendants for each node in a tree
NJTree                  Generate a neighbour joining tree
NPartitionPairs         Distributions of tips consistent with a
                        partition pair
NRooted                 Number of trees
NSplits                 Number of distinct splits
NTip                    Number of leaves in a phylogenetic tree
NewickTree              Write Newick Tree
NodeDepth               Distance of each node from tree exterior
NodeOrder               Order of each node in a tree
PairwiseDistances       Distances between each pair of trees
PolarizeSplits          Polarize splits on a single taxon
ReadCharacters          Read phylogenetic characters from file
ReadTntTree             Parse TNT Tree
Renumber                Renumber a tree's nodes and tips
RenumberTips            Renumber a tree's tips
RightmostCharacter      Rightmost character of string
RootNode                Which node is a tree's root?
RootTree                Root or unroot a phylogenetic tree
SingleTaxonTree         Generate a single taxon tree
SortTree                Sort tree
SplitFrequency          Frequency of splits
SplitInformation        Phylogenetic information content of splitting
                        leaves into two partitions
SplitMatchProbability   Probability of matching this well
Splits                  Convert object to 'Splits'
SplitsInBinaryTree      Maximum splits in an _n_-leaf tree
Stemwardness            'Stemwardness' of a leaf
StringToPhyDat          Convert between strings and 'phyDat' objects
Subsplit                Subset of a split on fewer leaves
Subtree                 Extract a subtree
SupportColour           Colour for node support value
TipLabels               Extract tip labels
TipsInSplits            Tips contained within splits
TotalCopheneticIndex    Total Cophenetic Index
TreeIsRooted            Is tree rooted?
TreeNumber              Unique integer indices for bifurcating tree
                        topologies
TreesMatchingSplit      Number of trees matching a bipartition split
TreesMatchingTree       Number of trees containing a tree
TrivialSplits           Identify and remove trivial splits
Unquote                 Remove quotation marks from a string
UnrootedTreesMatchingSplit
                        Number of trees consistent with split
UnshiftTree             Add tree to start of list
WriteTntCharacters      Write morphological character matrix to TNT
                        file
as.Newick               Write a phylogenetic tree in Newick format
as.multiPhylo           Convert object to 'multiPhylo' class
brewer                  Brewer palettes
doubleFactorials        Double factorials
logDoubleFactorials     Natural logarithms of double factorials
match                   Split matching
nRootedShapes           Number of rooted / unrooted tree shapes
print.TreeNumber        Print 'TreeNumber' object
sapply64                Apply a function that returns 64-bit integers
                        over a list or vector
