AllSplitPairings |
Variation of information for all split pairings |
cluster-statistics |
Cluster size statistics |
ClusteringEntropy |
Information content of splits within a tree |
ClusteringEntropy.list |
Information content of splits within a tree |
ClusteringEntropy.multiPhylo |
Information content of splits within a tree |
ClusteringEntropy.phylo |
Information content of splits within a tree |
ClusteringEntropy.Splits |
Information content of splits within a tree |
ClusteringInfo |
Information content of splits within a tree |
ClusteringInfo.list |
Information content of splits within a tree |
ClusteringInfo.multiPhylo |
Information content of splits within a tree |
ClusteringInfo.phylo |
Information content of splits within a tree |
ClusteringInfo.Splits |
Information content of 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 |
ConsensusInfo |
Information content of splits within a tree |
DifferentPhylogeneticInfo |
Information-based generalized Robinson–Foulds distances |
DistanceFromMedian |
Cluster size statistics |
DistFromMed |
Cluster size statistics |
Entropy |
Entropy in bits |
ExpectedVariation |
Information-based generalized Robinson–Foulds distances |
GetParallel |
Calculate distances in parallel |
InfoRobinsonFoulds |
Robinson–Foulds distances, with adjustments for phylogenetic information content |
InfoRobinsonFouldsSplits |
Robinson–Foulds distances, with adjustments for phylogenetic information content |
Islands |
Find islands from distance matrix |
JaccardRobinsonFoulds |
Jaccard–Robinson–Foulds metric |
JaccardSplitSimilarity |
Jaccard–Robinson–Foulds metric |
KCDiameter |
Kendall–Colijn distance |
KCVector |
Kendall–Colijn distance |
KendallColijn |
Kendall–Colijn distance |
KMeansPP |
k-means++ clustering |
LAPJV |
Solve linear assignment problem using LAPJV |
LnTreesConsistentWithTwoSplits |
Shared information content of two splits |
Log2TreesConsistentWithTwoSplits |
Shared information content of two splits |
MappingQuality |
Faithfulness of mapped distances |
MapTrees |
Graphical user interface for mapping distances and analysing tree space |
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 |
MeanCentDist |
Cluster size statistics |
MeanCentroidDist |
Cluster size statistics |
MeanCentroidDistance |
Cluster size statistics |
MeanMSTEdge |
Cluster size statistics |
MeanNN |
Cluster size statistics |
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 |
MSTSegments |
Add minimum spanning tree to plot, colouring by stress |
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 |
PathVector |
Kendall–Colijn distance |
PhylogeneticInfoDistance |
Information-based generalized Robinson–Foulds distances |
Plot3 |
Pseudo-3D plotting |
Project |
Graphical user interface for mapping distances and analysing tree space |
ProjectionQuality |
Faithfulness of mapped distances |
ReduceTrees |
Collapse areas of agreement between two trees |
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 |
SetParallel |
Calculate distances in parallel |
SharedPhylogeneticInfo |
Information-based generalized Robinson–Foulds distances |
SharedPhylogeneticInfoSplits |
Information-based generalized Robinson–Foulds distances |
SpectralClustering |
Eigenvalues for spectral clustering |
SpectralEigens |
Eigenvalues for spectral clustering |
SplitDifferentInformation |
Shared information content of two splits |
SplitEntropy |
Entropy of two splits |
SplitsCompatible |
Are splits compatible? |
SplitSharedInformation |
Shared information content of two splits |
SplitVector |
Kendall–Colijn distance |
SplitwiseInfo |
Information content of splits within a tree |
SPRDist |
Approximate the Subtree Prune and Regraft (SPR) distance. |
SPRDist.list |
Approximate the Subtree Prune and Regraft (SPR) distance. |
SPRDist.multiPhylo |
Approximate the Subtree Prune and Regraft (SPR) distance. |
SPRDist.phylo |
Approximate the Subtree Prune and Regraft (SPR) distance. |
StartParallel |
Calculate distances in parallel |
StopParallel |
Calculate distances in parallel |
StrainCol |
Add minimum spanning tree to plot, colouring by stress |
SumOfRanges |
Cluster size statistics |
SumOfVariances |
Cluster size statistics |
SumOfVars |
Cluster size statistics |
TreeDistance |
Information-based generalized Robinson–Foulds distances |
TreeInfo |
Information content of splits within a tree |
TreesConsistentWithTwoSplits |
Shared information content of two splits |
VisualizeMatching |
Visualise a matching |