# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "TreeSearch" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'TreeSearch: Phylogenetic Analysis with Discrete Character Data'
version: 1.5.1.9000
identifiers:
- type: doi
  value: 10.32614/CRAN.package.TreeSearch
- type: url
  value: https://github.com/ms609/TreeSearch/
abstract: Reconstruct phylogenetic trees from discrete data. Inapplicable character
  states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) <https://doi.org/10.1093/sysbio/syy083>
  with the "Morphy" library, under equal or implied step weights. Contains a "shiny"
  user interface for interactive tree search and exploration of results, including
  character visualization, rogue taxon detection, tree space mapping, and cluster
  consensus trees (Smith 2022a, b) <https://doi.org/10.1093/sysbio/syab099>, <https://doi.org/10.1093/sysbio/syab100>.
  Profile Parsimony (Faith and Trueman, 2001) <https://doi.org/10.1080/10635150118627>,
  Successive Approximations (Farris, 1969) <https://doi.org/10.2307/2412182> and custom
  optimality criteria are implemented.
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: manual
  title: 'MorphyLib: a library for phylogenetic analysis of categorical trait data
    with inapplicability'
  authors:
  - family-names: Brazeau
    given-names: Martin D.
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
    orcid: https://orcid.org/0000-0001-5660-1727
  - family-names: Guillerme
    given-names: Thomas
  year: '2017'
  notes: Version 0.0.1-alpha
repository: https://phylotastic.r-universe.dev
repository-code: https://github.com/ms609/TreeSearch/issues/
commit: bfd90c885ae08d4199c8d993f3e7fb97a4d6b70e
url: https://ms609.github.io/TreeSearch/
contact:
- family-names: Smith
  given-names: Martin R.
  email: martin.smith@durham.ac.uk
  orcid: https://orcid.org/0000-0001-5660-1727
references:
- type: article
  title: An algorithm for morphological phylogenetic analysis with inapplicable data
  authors:
  - family-names: Brazeau
    given-names: Martin D.
  - family-names: Guillerme
    given-names: Thomas
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
  journal: Systematic Biology
  volume: '64'
  issue: '4'
  year: '2019'
  start: 619-631
- type: manual
  title: 'TreeSearch: phylogenetic analysis with discrete character data'
  authors:
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
  notes: R package version 1.5.1.9000
  year: '2018'
  doi: 10.5281/zenodo.1042590
- type: article
  title: 'TreeSearch: morphological phylogenetic analysis in R'
  authors:
  - family-names: Smith
    given-names: Martin R.
    email: martin.smith@durham.ac.uk
  year: '2023'
  journal: R Journal
  volume: '14'
  issue: '4'
  doi: 10.32614/RJ-2023-019
  start: 305-315