AddTip                  Add a tip to a phylogenetic tree
AllAncestors            List all ancestral nodes
ApeTime                 Ape Time
BalancedTree            Generate a Balanced Tree
CharacterInformation    Character information content
CollapseNode            Collapse nodes on a phylogenetic tree
ConsensusWithout        Consensus without taxa
DescendantEdges         Descendant Edges
DoubleFactorial         Double Factorial
EdgeAncestry            Edge ancestry
EdgeDistances           Distance between edges
EnforceOutgroup         Force taxa to form an outgroup
Lobo.data               Raw data from Zhang et al. 2016
Lobo.phy                Data from Zhang et al. 2016 in 'phyDat' format
MRCA                    Most Recent Common Ancestor
N1Spr                   Number of trees one SPR step away
NJTree                  Neighbour Joining Tree
NPartitionPairs         Distributions of tips consistent with a
                        partition pair
NRooted                 Number of rooted/unrooted trees
NSplits                 Number of distinct partitions
NTip                    Number of tips in a phylogenetic tree
NewickTree              Newick Tree
PectinateTree           Generate a Pectinate Tree
PhyToString             'phyDat' to String
RandomTree              Generate a random tree topology
ReadCharacters          Read characters from Nexus file
ReadTntTree             Parse TNT Tree
Renumber                Renumber a tree's nodes and tips
RenumberTips            Renumber a tree's tips
RootTree                Root a phylogenetic tree
SingleTaxonTree         Single Taxon Tree
SortTree                Sort tree
SplitFrequency          Frequency of splits
SplitInformation        Information content of a split
SplitMatchProbability   Probability of matching this well
StringToPhyDat          String to 'phyDat'
Subsplit                Subset of a split on fewer taxa
Subtree                 Extract subtree
SupportColour           Support colour
TipLabels               Extract tip labels
TipsInSplits            Tips contained within splits
TreeIsRooted            Is tree rooted?
TreeNumber              Unique integer indices for bifurcating tree
                        topologies
TreesMatchingSplit      Number of trees matching a bipartition split
TrivialSplits           Are splits trivial?
UnrootedTreesMatchingSplit
                        Number of trees consistent with split
UnshiftTree             Add Tree to Start of List
as.Newick               Write a phylogenetic tree in Newick format
as.Splits               As splits
brewer                  Brewer palettes
doubleFactorials        Double factorials
in.Splits               Splits in Splits object
logDoubleFactorials     Natural logarithms of double factorials
match.Splits            Match splits
print.TreeNumber        Print 'TreeNumber' object
