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TreeDist: Distances Between Phylogenetic Trees

Name: TreeDist: Distances Between Phylogenetic Trees
Creator: Martin R. Smith
Keywords: phylogenetic trees, phylogenetics, tree space, tree distance, R packages, R, distance metrics

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 04 Nov 2019 English Publisher:Zenodo

Authors: Martin R. Smith;

TreeDist: Distances Between Phylogenetic Trees

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Abstract

An R package that 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>. Calculates the median of a set of trees under any distance metric. Details and installation instructions are available at ms609.github.io/TreeDist.

Related Organizations

Durham University
United Kingdom

Keywords

phylogenetic trees, phylogenetics, tree space, tree distance, R packages, R, distance metrics

1 Research products, page 1 of 1

ms609/TreeDist: v2.10.0
2022IsVersionOf

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