Calculate and Map Distances Between Phylogenetic Trees
Variation of information for all split pairings
Wrapper for tree distance calculations
Cluster size statistics
Distances between each pair of trees
Calculate MAST size from edge matrices.
Mean of two numbers
Calculate distance between trees, or lists of trees
Entropy in bits
Generalized Robinson–Foulds distance
Find islands from distance matrix
Jaccard–Robinson–Foulds metric
Kendall–Colijn distance
k-means++ clustering
Solve linear assignment problem using LAPJV
Faithfulness of mapped distances
Graphical user interface for mapping distances and analysing tree spac...
Maximum Agreement Subtree size
Matching Split Distance
Median of a set of trees
Use variation of clustering information to compare pairs of splits
Add minimum spanning tree to plot, colouring by stress
Approximate Nearest Neighbour Interchange distance
Normalize tree distances
Nye et al. (2006) tree comparison
Path distance
Pseudo-3D plotting
Collapse areas of agreement between two trees
List clades as text
Robinson–Foulds distances, with adjustments for phylogenetic informati...
Eigenvalues for spectral clustering
Entropy of two splits
Are splits compatible?
Shared information content of two splits
Approximate the Subtree Prune and Regraft (SPR) distance.
Calculate distances in parallel
TreeDist: Distances between Phylogenetic Trees
Information-based generalized Robinson–Foulds distances
Plot a simple tree
Information content of splits within a tree
Visualize a matching
Implements measures of tree similarity, including information-based generalized Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information Distance, Matching Split Information Distance; Smith 2020) <doi:10.1093/bioinformatics/btaa614>; Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <doi:10.1007/978-3-642-40453-5_13>, including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>; the Matching Split Distance (Bogdanowicz & Giaro 2012) <doi:10.1109/TCBB.2011.48>; Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al. (1996) <doi:10.1007/3-540-61332-3_168>. Includes tools for visualizing mappings of tree space (Smith 2022) <doi:10.1093/sysbio/syab100>, for identifying islands of trees (Silva and Wilkinson 2021) <doi:10.1093/sysbio/syab015>, for calculating the median of sets of trees, and for computing the information content of trees and splits.
Useful links