TreeDist
Calculate and Map Distances Between Phylogenetic Trees
Last update: 25 October 2023
Software version identifier: 2.6.0, 2.6.1, 1.0.0, 1.1.1, 1.2.0, 1.2.1, 2.0.0, 2.0.2, 2.0.3, 2.1.0, 2.1.1, 2.2.0, 2.3.0, 2.4.0, 2.4.1, 2.5.0, 2.6.2, 2.6.3, 2.7.0
Copyright license: GNU General Public License
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 calculating the median of sets of trees, and for computing the information content of trees and splits.
- Robust Analysis of Phylogenetic Tree Space
- Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees
- The Generalized Robinson-Foulds Metric
- A novel algorithm and web-based tool for comparing two alternative phylogenetic trees
- Matching Split Distance for Unrooted Binary Phylogenetic Trees
- Mapping Phylogenetic Trees to Reveal Distinct Patterns of Evolution
- Some notes on the nearest neighbour interchange distance
