TreeDist

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.

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