AllSplitPairings        Variation of information for all split pairings
CompareAll              Distances between each pair of trees
Entropy                 Entropy in bits
HPart                   Hierarchical partition structure
HierarchicalMutualInfo
                        Hierarchical Mutual Information
Islands                 Find islands from distance matrix
JaccardRobinsonFoulds   Jaccard–Robinson–Foulds metric
KMeansPP                k-means++ clustering
KendallColijn           Kendall–Colijn distance
LAPJV                   Solve linear assignment problem using LAPJV
MASTSize                Maximum Agreement Subtree size
MSTSegments             Add minimum spanning tree to plot, colouring by
                        stress
MapTrees                Graphical user interface for mapping distances
                        and analysing tree space
MappingQuality          Faithfulness of mapped distances
MatchingSplitDistance   Matching Split Distance
MeilaVariationOfInformation
                        Use variation of clustering information to
                        compare pairs of splits
NNIDist                 Approximate Nearest Neighbour Interchange
                        distance
NyeSimilarity           Nye _et al_. (2006) tree comparison
PathDist                Path distance
Plot3                   Pseudo-3D plotting
ReduceTrees             Collapse areas of agreement between two trees
Robinson-Foulds         Robinson–Foulds distances, with adjustments for
                        phylogenetic information content
SPRDist                 Approximate the Subtree Prune and Regraft
                        distance
SpectralEigens          Eigenvalues for spectral clustering
SplitEntropy            Entropy of two splits
SplitSharedInformation
                        Shared information content of two splits
SplitsCompatible        Are splits compatible?
StartParallel           Calculate distances in parallel
TreeDistance            Information-based generalized Robinson–Foulds
                        distances
TreeInfo                Information content of splits within a tree
VisualizeMatching       Visualize a matching
cluster-statistics      Cluster size statistics
median.multiPhylo       Median of a set of trees
