# Distances Between Phylogenetic Trees

## Documentation for package ‘TreeDist’ version 1.1.1

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

## Help Pages

AllSplitPairings | Variation of information for all split pairings
ClusteringEntropy | Clustering entropy of all splits within a tree
ClusteringEntropy.list | Clustering entropy of all splits within a tree
ClusteringEntropy.multiPhylo | Clustering entropy of all splits within a tree
ClusteringEntropy.phylo | Clustering entropy of all splits within a tree
ClusteringEntropy.Splits | Clustering entropy of all splits within a tree
ClusteringInfo | Clustering entropy of all splits within a tree
ClusteringInfo.list | Clustering entropy of all splits within a tree
ClusteringInfo.multiPhylo | Clustering entropy of all splits within a tree
ClusteringInfo.phylo | Clustering entropy of all splits within a tree
ClusteringInfo.Splits | Clustering entropy of all splits within a tree
ClusteringInfoDist | Information-based generalized Robinson-Foulds distances
ClusteringInfoDistance | Information-based generalized Robinson-Foulds distances
CompareAll | Distances between each pair of trees
DifferentPhylogeneticInfo | Information-based generalized Robinson-Foulds distances
Entropy | Entropy in bits
ExpectedVariation | Information-based generalized Robinson-Foulds distances
InfoRobinsonFoulds | Robinson-Foulds distances, with adjustments for phylogenetic information content
InfoRobinsonFouldsSplits | Robinson-Foulds distances, with adjustments for phylogenetic information content
JaccardRobinsonFoulds | Jaccard-Robinson-Foulds metric
JaccardSplitSimilarity | Jaccard-Robinson-Foulds metric
KCVector | Kendall-Colijn distance
KendallColijn | Kendall-Colijn distance
LAPJV | Solve linear assignment problem using LAPJV
LnTreesConsistentWithTwoSplits | Shared information content of two splits
MASTInfo | Maximum Agreement Subtree size
MASTSize | Maximum Agreement Subtree size
MatchingSplitDistance | Matching Split Distance
MatchingSplitDistanceSplits | Matching Split Distance
MatchingSplitInfo | Information-based generalized Robinson-Foulds distances
MatchingSplitInfoDistance | Information-based generalized Robinson-Foulds distances
MatchingSplitInfoSplits | Information-based generalized Robinson-Foulds distances
median.multiPhylo | Median of a set of trees
MeilaMutualInformation | Use variation of clustering information to compare pairs of splits
MeilaVariationOfInformation | Use variation of clustering information to compare pairs of splits
MutualClusteringInfo | Information-based generalized Robinson-Foulds distances
MutualClusteringInformation | Information-based generalized Robinson-Foulds distances
MutualClusteringInfoSplits | Information-based generalized Robinson-Foulds distances
NNIDiameter | Approximate Nearest Neighbour Interchange distance
NNIDist | Approximate Nearest Neighbour Interchange distance
NyeSimilarity | Nye _et al_. (2006) tree comparison
NyeSplitSimilarity | Nye _et al_. (2006) tree comparison
PathDist | Path distance
PhylogeneticInfoDistance | Information-based generalized Robinson-Foulds distances
Robinson-Foulds | Robinson-Foulds distances, with adjustments for phylogenetic information content
RobinsonFoulds | Robinson-Foulds distances, with adjustments for phylogenetic information content
RobinsonFouldsInfo | Robinson-Foulds distances, with adjustments for phylogenetic information content
RobinsonFouldsMatching | Robinson-Foulds distances, with adjustments for phylogenetic information content
RobinsonFouldsSplits | Robinson-Foulds distances, with adjustments for phylogenetic information content
SharedPhylogeneticInfo | Information-based generalized Robinson-Foulds distances
SharedPhylogeneticInfoSplits | Information-based generalized Robinson-Foulds distances
SplitDifferentInformation | Shared information content of two splits
SplitEntropy | Entropy of two splits
SplitsCompatible | Are splits compatible?
SplitSharedInformation | Shared information content of two splits
SplitwiseInfo | Information content of splits within a tree
SPRDist | Approximate Subtree Prune and Regraft distance
TreeDistance | Information-based generalized Robinson-Foulds distances
TreesConsistentWithTwoSplits | Shared information content of two splits
VisualizeMatching | Visualise a matching