AddTip                  Add a tip to a phylogenetic tree
ApeTime                 Read modification time from "ape" Nexus file
ArtificialExtinction    Artificial Extinction
CharacterInformation    Character information content
Cherries                Count cherries in a tree
CladeSizes              Clade sizes
CladisticInfo           Cladistic information content of a tree
ClusterTable            Convert phylogenetic tree to 'ClusterTable'
ClusterTable-methods    S3 methods for 'ClusterTable' objects
CollapseNode            Collapse nodes on a phylogenetic tree
Consensus               Construct consensus trees
ConsensusWithout        Reduced consensus, omitting specified taxa
ConstrainedNJ           Constrained neighbour-joining tree
Decompose               Decompose additive (ordered) phylogenetic
                        characters
DescendantEdges         Identify descendant edges
DoubleFactorial         Double factorial
DropTip                 Drop leaves from tree
EdgeAncestry            Ancestors of an edge
EdgeDistances           Distance between edges
EdgeRatio               Ratio of external:internal edge length
EndSentence             Add full stop to end of a sentence
GenerateTree            Generate pectinate, balanced or random trees
Hamming                 Hamming distance between taxa in a phylogenetic
                        dataset
ImposeConstraint        Force a tree to match a constraint
J1Index                 Robust universal tree balance index
KeptPaths               Paths present in reduced tree
KeptVerts               Identify vertices retained when leaves are
                        dropped
LabelSplits             Label splits
LeafLabelInterchange    Leaf label interchange
ListAncestors           List ancestors
Lobo.data               Data from Zhang et al. 2016
LongBranch              Identify taxa with long branches
MRCA                    Most recent common ancestor
MSTEdges                Minimum spanning tree
MakeTreeBinary          Generate binary tree by collapsing polytomies
MatchEdges              Match nodes and edges between trees
MatchStrings            Check for mismatch between character vectors
MatrixToPhyDat          Convert between matrices and 'phyDat' objects
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
NexusTokensToInteger    Convert Nexus token matrix to integer
NodeDepth               Distance of each node from tree exterior
NodeNumbers             Numeric index of each node in a tree
                        'NodeNumbers()' returns a sequence
                        corresponding to the nodes in a tree
NodeOrder               Number of edges incident to each node in a tree
PaintTree               Colour a tree by topology
PairwiseDistances       Distances between each pair of trees
PathLengths             Calculate length of paths between each pair of
                        vertices within tree
PolarizeSplits          Polarize splits on a single taxon
ReadCharacters          Read phylogenetic characters from file
ReadMrBayesTrees        Read posterior tree sample produced by MrBayes
ReadTntTree             Parse TNT Tree
Renumber                Renumber a tree's nodes and tips
RenumberTips            Renumber a tree's tips
Reweight                Re-weight phylogenetic characters
RightmostCharacter      Rightmost character of string
RoguePlot               Visualize position of rogue taxa
RootNode                Which node is a tree's root?
RootTree                Root or unroot a phylogenetic tree
SampleOne               Select element at random
SortTree                Sort tree
SplitConsistent         Identify consistent / conflicting splits
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
TipTimedTree            Display time-calibrated tree using tip
                        information only
TipsInSplits            Tips contained within splits
TopologyOnly            Remove metadata from trees
TotalCopheneticIndex    Total Cophenetic Index
TreeIsRooted            Is tree rooted?
TreeNumber              Unique integer indices for bifurcating tree
                        topologies
Treeness                Relative length of internal branches
TreesMatchingSplit      Number of trees matching a bipartition split
TreesMatchingTree       Number of trees containing a tree
TrivialSplits           Identify and remove trivial splits
TrivialTree             Generate trivial trees
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
edge_to_splits          Efficiently convert edge matrix to splits
is.TreeNumber           Is an object a 'TreeNumber' object?
logDoubleFactorials     Natural logarithms of double factorials
match,Splits,Splits-method
                        Split matching
match,phylo,phylo-method
                        Tree 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
sort.multiPhylo         Sort a list of phylogenetic trees
xor                     Exclusive OR operation
