# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "TBRDist" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'TBRDist: Rearrangement Distances Between Phylogenetic Trees'
version: 2.0.1
doi: 10.1137/110845045
identifiers:
- type: doi
  value: 10.32614/CRAN.package.TBRDist
- type: url
  value: https://github.com/ms609/TBRDist/
- type: url
  value: https://github.com/cwhidden/uspr/
- type: url
  value: https://github.com/cwhidden/rspr/
abstract: 'Fast calculation of tree rearrangement distances. For unrooted trees: Subtree
  Prune and Regraft (SPR), Tree Bisection and Reconnection (TBR), and Replug distances,
  using the algorithms of Whidden and Matsen (2017) <https://doi.org/10.48550/arXiv.1511.07529>.
  For rooted trees: rooted SPR (rSPR) distance, using the fixed-parameter algorithms
  of Whidden, Beiko, and Zeh (2013) <https://doi.org/10.1137/110845045>.'
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: Fixed-Parameter Algorithms for Maximum Agreement Forests
  authors:
  - family-names: Whidden
    given-names: Chris
  - family-names: Beiko
    given-names: RG
  - family-names: Zeh
    given-names: 'N'
  year: '2013'
  journal: SIAM Journal on Computing
  volume: '42'
  doi: 10.1137/110845045
  start: 1431-–1466
repository: https://cran.r-universe.dev
repository-code: https://github.com/ms609/TBRDist/issues/
commit: c7cab38a5705a466dc956fcdcb9e018a5d952039
url: https://ms609.github.io/TBRDist/
date-released: '2026-07-21'
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: Calculating the Unrooted Subtree-Prune-and-Regraft Distance.
  authors:
  - family-names: Whidden
    given-names: Chris
  - family-names: Matsen
    given-names: Frederick A.
  journal: IEEE/ACM Transactions on Computational Biology and Bioinformatics
  issue: '3'
  volume: '16'
  year: '2019'
  doi: 10.1109/TCBB.2018.2802911
  start: '898'
  end: '911'
- type: article
  title: Supertrees based on the subtree prune-and-regraft distance
  authors:
  - family-names: Whidden
    given-names: Chris
  - family-names: Zeh
    given-names: 'N'
  - family-names: Beiko
    given-names: RG
  year: '2014'
  journal: Systematic Biology
  volume: '63'
  doi: 10.1093/sysbio/syu023
  start: '566'
  end: '581'
- type: manual
  title: 'TBRDist: Rearrangement Distances Between Phylogenetic Trees'
  authors:
  - family-names: Smith
    given-names: Martin R.
  notes: R package version 2.0.1
  publisher:
    name: Comprehensive R Archive Network
  year: '2019'
  doi: 10.5281/zenodo.3548333