Tree distance measuresFunctions for calculating distances between pairs of trees. |
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Information-based generalized Robinson–Foulds distances |
Nye et al. (2006) tree comparison |
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Kendall–Colijn distance |
Matching Split Distance |
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Jaccard–Robinson–Foulds metric |
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Maximum Agreement Subtree size |
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Approximate Nearest Neighbour Interchange distance |
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Path distance |
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Robinson–Foulds distances, with adjustments for phylogenetic information content |
Approximate Subtree Prune and Regraft distance |
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Distances between each pair of trees |
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Visualise a matching |
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Tree spaceFunctions for the construction, evaluation and exploration of tree space. |
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Add minimum spanning tree to plot, colouring by stress |
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Graphical user interface for mapping distances and analysing tree space |
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Faithfulness of mapped distances |
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Eigenvalues for spectral clustering |
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Cluster size statistics |
Median of a set of trees |
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Pseudo-3D plotting |
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Cluster analysisFunctions for identifying and interrogating clusters of trees. |
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Cluster size statistics |
k-means++ clustering |
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InformationFunctions addressing the information content and entropy of splits. |
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Variation of information for all split pairings |
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Entropy in bits |
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Use variation of clustering information to compare pairs of splits |
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Are splits compatible? |
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Entropy of two splits |
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Shared information content of two splits |
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Information content of splits within a tree |
Utility functionsFunctions to facilitate interaction with the package. |
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Distances between each pair of trees |
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Solve linear assignment problem using LAPJV |
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Pseudo-3D plotting |
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Calculate distances in parallel |
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Visualise a matching |