# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "TreeDist" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'TreeDist: Calculate and Map Distances Between Phylogenetic Trees'
version: 2.14.1
doi: 10.1093/bioinformatics/btaa614
identifiers:
- type: doi
  value: 10.32614/CRAN.package.TreeDist
- type: url
  value: https://github.com/ms609/TreeDist/
abstract: Implements measures of tree similarity, including information-based generalized
  Robinson-Foulds distances (Phylogenetic Information Distance, Clustering Information
  Distance, Matching Split Information Distance; Smith 2020) <https://doi.org/10.1093/bioinformatics/btaa614>;
  Jaccard-Robinson-Foulds distances (Bocker et al. 2013) <https://doi.org/10.1007/978-3-642-40453-5_13>,
  including the Nye et al. (2006) metric <https://doi.org/10.1093/bioinformatics/bti720>;
  the Matching Split Distance (Bogdanowicz & Giaro 2012) <https://doi.org/10.1109/TCBB.2011.48>;
  the Hierarchical Mutual Information (Perotti et al. 2015) <https://doi.org/10.1103/PhysRevE.92.062825>;
  Maximum Agreement Subtree distances; the Kendall-Colijn (2016) distance <https://doi.org/10.1093/molbev/msw124>,
  and the Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
  (1996) <https://doi.org/10.1007/3-540-61332-3_168>. Includes tools for visualizing
  mappings of tree space (Smith 2022) <https://doi.org/10.1093/sysbio/syab100>, for
  identifying islands of trees (Silva and Wilkinson 2021) <https://doi.org/10.1093/sysbio/syab015>,
  for calculating the median of sets of trees, and for computing the information content
  of trees and splits.
authors:
- family-names: Smith
  given-names: Martin R.
  email: martin.smith@durham.ac.uk
  orcid: https://orcid.org/0000-0001-5660-1727
preferred-citation:
  type: article
  title: Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic
    trees
  authors:
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
    orcid: https://orcid.org/0000-0001-5660-1727
  doi: 10.1093/bioinformatics/btaa614
  journal: Bioinformatics
  volume: '36'
  issue: '20'
  year: '2020'
  start: 5007–5013
repository: https://cran.r-universe.dev
repository-code: https://github.com/ms609/TreeDist/issues/
commit: 0f8eb0426fa075f9d10776e85e1a3317cd7ed41e
url: https://ms609.github.io/TreeDist/
date-released: '2026-06-10'
contact:
- family-names: Smith
  given-names: Martin R.
  email: martin.smith@durham.ac.uk
  orcid: https://orcid.org/0000-0001-5660-1727
keywords:
- phylogenetics
- tree-distance
references:
- type: article
  title: Robust analysis of phylogenetic tree space
  authors:
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
  doi: 10.1093/sysbio/syab100
  journal: Systematic Biology
  volume: '71'
  issue: '5'
  year: '2022'
  start: 1255-1270
- type: manual
  title: 'TreeDist: Distances between Phylogenetic Trees. R package version 2.14.1'
  authors:
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
  doi: 10.5281/zenodo.3528124
  journal: Comprehensive R Archive Network
  year: '2020'