# --------------------------------------------
# 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 "ape" in publications use:'
type: software
license:
- GPL-2.0-only
- GPL-3.0-only
title: 'ape: Analyses of Phylogenetics and Evolution'
version: 5.8-0.2
doi: 10.1093/bioinformatics/bty633
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ape
abstract: Functions for reading, writing, plotting, and manipulating phylogenetic
  trees, analyses of comparative data in a phylogenetic framework, ancestral character
  analyses, analyses of diversification and macroevolution, computing distances from
  DNA sequences, reading and writing nucleotide sequences as well as importing from
  BioConductor, and several tools such as Mantel's test, generalized skyline plots,
  graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of
  absolute evolutionary rates and clock-like trees using mean path lengths and penalized
  likelihood, dating trees with non-contemporaneous sequences, translating DNA into
  AA sequences, and assessing sequence alignments. Phylogeny estimation can be done
  with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling
  incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle
  method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle)
  whose results are returned into R.
authors:
- family-names: Paradis
  given-names: Emmanuel
  email: Emmanuel.Paradis@ird.fr
  orcid: https://orcid.org/0000-0003-3092-2199
- family-names: Blomberg
  given-names: Simon
  orcid: https://orcid.org/0000-0003-1062-0839
- family-names: Bolker
  given-names: Ben
  orcid: https://orcid.org/0000-0002-2127-0443
- family-names: Brown
  given-names: Joseph
  orcid: https://orcid.org/0000-0002-3835-8062
- family-names: Claramunt
  given-names: Santiago
  orcid: https://orcid.org/0000-0002-8926-5974
- family-names: Claude
  given-names: Julien
  orcid: https://orcid.org/0000-0002-9267-1228
- family-names: Cuong
  given-names: Hoa Sien
- family-names: Desper
  given-names: Richard
- family-names: Didier
  given-names: Gilles
  orcid: https://orcid.org/0000-0003-0596-9112
- family-names: Durand
  given-names: Benoit
- family-names: Dutheil
  given-names: Julien
  orcid: https://orcid.org/0000-0001-7753-4121
- family-names: Ewing
  given-names: RJ
- family-names: Gascuel
  given-names: Olivier
- family-names: Guillerme
  given-names: Thomas
  orcid: https://orcid.org/0000-0003-4325-1275
- family-names: Heibl
  given-names: Christoph
  orcid: https://orcid.org/0000-0002-7655-3299
- family-names: Ives
  given-names: Anthony
  orcid: https://orcid.org/0000-0001-9375-9523
- family-names: Jones
  given-names: Bradley
  orcid: https://orcid.org/0000-0003-4498-1069
- family-names: Krah
  given-names: Franz
  orcid: https://orcid.org/0000-0001-7866-7508
- family-names: Lawson
  given-names: Daniel
  orcid: https://orcid.org/0000-0002-5311-6213
- family-names: Lefort
  given-names: Vincent
- family-names: Legendre
  given-names: Pierre
  orcid: https://orcid.org/0000-0002-3838-3305
- family-names: Lemon
  given-names: Jim
- family-names: Louvel
  given-names: Guillaume
  orcid: https://orcid.org/0000-0002-7745-0785
- family-names: Marcon
  given-names: Eric
  orcid: https://orcid.org/0000-0002-5249-321X
- family-names: McCloskey
  given-names: Rosemary
  orcid: https://orcid.org/0000-0002-9772-8553
- family-names: Nylander
  given-names: Johan
- family-names: Opgen-Rhein
  given-names: Rainer
- family-names: Popescu
  given-names: Andrei-Alin
- family-names: Royer-Carenzi
  given-names: Manuela
- family-names: Schliep
  given-names: Klaus
  orcid: https://orcid.org/0000-0003-2941-0161
- family-names: Strimmer
  given-names: Korbinian
  orcid: https://orcid.org/0000-0001-7917-2056
- family-names: Vienne
  given-names: Damien
  name-particle: de
  orcid: https://orcid.org/0000-0001-9532-5251
preferred-citation:
  type: article
  title: 'ape 5.0: an environment for modern phylogenetics and evolutionary analyses
    in R'
  authors:
  - family-names: Paradis
    given-names: Emmanuel
    email: Emmanuel.Paradis@ird.fr
    orcid: https://orcid.org/0000-0003-3092-2199
  - family-names: Schliep
    given-names: Klaus
    orcid: https://orcid.org/0000-0003-2941-0161
  journal: Bioinformatics
  year: '2019'
  volume: '35'
  doi: 10.1093/bioinformatics/bty633
  start: 526-528
repository: https://emmanuelparadis.r-universe.dev
repository-code: https://github.com/emmanuelparadis/ape
commit: 6d4fb5467734b4f9a6ae7165929d26cf9040ba35
url: https://github.com/emmanuelparadis/ape
date-released: '2024-07-22'
contact:
- family-names: Paradis
  given-names: Emmanuel
  email: Emmanuel.Paradis@ird.fr
  orcid: https://orcid.org/0000-0003-3092-2199