Man pages for TreeDist
Calculate and Map Distances Between Phylogenetic Trees
| AllSplitPairings | Variation of information for all split pairings |
| CalculateTreeDistance | Wrapper for tree distance calculations |
| cluster-statistics | Cluster size statistics |
| CompareAll | Distances between each pair of trees |
| dot-MASTSizeEdges | Calculate MAST size from edge matrices. |
| dot-PairMean | Mean of two numbers |
| dot-TreeDistance | Calculate distance between trees, or lists of trees |
| Entropy | Entropy in bits |
| entropy_int | Calculate entropy of integer vector of counts |
| GeneralizedRF | Generalized Robinson–Foulds distance |
| Islands | Find islands from distance matrix |
| JaccardRobinsonFoulds | Jaccard–Robinson–Foulds metric |
| KendallColijn | Kendall–Colijn distance |
| KMeansPP | k-means++ clustering |
| LAPJV | Solve linear assignment problem using LAPJV |
| MappingQuality | Faithfulness of mapped distances |
| MapTrees | Graphical user interface for mapping distances and analysing... |
| MASTSize | Maximum Agreement Subtree size |
| MatchingSplitDistance | Matching Split Distance |
| median.multiPhylo | Median of a set of trees |
| MeilaVariationOfInformation | Use variation of clustering information to compare pairs of... |
| MSTSegments | Add minimum spanning tree to plot, colouring by stress |
| NNIDist | Approximate Nearest Neighbour Interchange distance |
| NormalizeInfo | Normalize tree distances |
| NyeSimilarity | Nye _et al_. (2006) tree comparison |
| PathDist | Path distance |
| Plot3 | Pseudo-3D plotting |
| ReduceTrees | Collapse areas of agreement between two trees |
| ReportMatching | List clades as text |
| Robinson-Foulds | Robinson–Foulds distances, with adjustments for phylogenetic... |
| SpectralEigens | Eigenvalues for spectral clustering |
| SplitEntropy | Entropy of two splits |
| SplitsCompatible | Are splits compatible? |
| SplitSharedInformation | Shared information content of two splits |
| SPRDist | Approximate the Subtree Prune and Regraft (SPR) distance. |
| StartParallel | Calculate distances in parallel |
| TreeDistance | Information-based generalized Robinson–Foulds distances |
| TreeDist-package | TreeDist: Distances between Phylogenetic Trees |
| TreeDistPlot | Plot a simple tree |
| TreeInfo | Information content of splits within a tree |
| VisualizeMatching | Visualize a matching |
