Man pages for ms609/TreeDist
Calculate and Map Distances Between Phylogenetic Trees

AllSplitPairingsVariation of information for all split pairings
CalculateTreeDistanceWrapper for tree distance calculations
cluster-statisticsCluster size statistics
CompareAllDistances between each pair of trees
dot-MASTSizeEdgesCalculate MAST size from edge matrices.
dot-PairMeanMean of two numbers
dot-TreeDistanceCalculate distance between trees, or lists of trees
EntropyEntropy in bits
GeneralizedRFGeneralized Robinson–Foulds distance
IslandsFind islands from distance matrix
JaccardRobinsonFouldsJaccard–Robinson–Foulds metric
KendallColijnKendall–Colijn distance
KMeansPPk-means++ clustering
LAPJVSolve linear assignment problem using LAPJV
MappingQualityFaithfulness of mapped distances
MapTreesGraphical user interface for mapping distances and analysing...
MASTSizeMaximum Agreement Subtree size
MatchingSplitDistanceMatching Split Distance
median.multiPhyloMedian of a set of trees
MeilaVariationOfInformationUse variation of clustering information to compare pairs of...
MSTSegmentsAdd minimum spanning tree to plot, colouring by stress
NNIDistApproximate Nearest Neighbour Interchange distance
NormalizeInfoNormalize tree distances
NyeSimilarityNye _et al_. (2006) tree comparison
PathDistPath distance
Plot3Pseudo-3D plotting
ReduceTreesCollapse areas of agreement between two trees
ReportMatchingList clades as text
Robinson-FouldsRobinson–Foulds distances, with adjustments for phylogenetic...
SpectralEigensEigenvalues for spectral clustering
SplitEntropyEntropy of two splits
SplitsCompatibleAre splits compatible?
SplitSharedInformationShared information content of two splits
SPRDistApproximate the Subtree Prune and Regraft (SPR) distance.
StartParallelCalculate distances in parallel
TreeDistanceInformation-based generalized Robinson–Foulds distances
TreeDist-packageTreeDist: Distances between Phylogenetic Trees
TreeDistPlotPlot a simple tree
TreeInfoInformation content of splits within a tree
VisualizeMatchingVisualize a matching
ms609/TreeDist documentation built on Sept. 13, 2024, 12:09 a.m.