Package: ape
Version: 5.8-3
Date: 2026-06-17
Title: Analyses of Phylogenetics and Evolution
Authors@R: c(person("Emmanuel", "Paradis", role = c("aut", "cre", "cph"), email = "Emmanuel.Paradis@ird.fr", comment = c(ORCID = "0000-0003-3092-2199")),
  person("Simon", "Blomberg", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-1062-0839")),
  person("Ben", "Bolker", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-2127-0443")),
  person("Joseph", "Brown", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-3835-8062")),
  person("Santiago", "Claramunt", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-8926-5974")),
  person("Julien", "Claude", role = c("aut", "cph"), , comment = c(ORCID = "0000-0002-9267-1228")),
  person("Hoa Sien", "Cuong", role = c("aut", "cph")),
  person("Richard", "Desper", role = c("aut", "cph")),
  person("Gilles", "Didier", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-0596-9112")),
  person("Benoit", "Durand", role = c("aut", "cph")),
  person("Julien", "Dutheil", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-7753-4121")),
  person("RJ", "Ewing", role = c("aut", "cph")),
  person("Olivier", "Gascuel", role = c("aut", "cph")),
  person("Thomas", "Guillerme", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-4325-1275")),
  person("Christoph", "Heibl", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-7655-3299")),
  person("Anthony", "Ives", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-9375-9523")),
  person("Bradley", "Jones", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-4498-1069")),
  person("Franz", "Krah", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-7866-7508")),
  person("Daniel", "Lawson", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-5311-6213")),
  person("Vincent", "Lefort", role = c("aut", "cph")),
  person("Pierre", "Legendre", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-3838-3305")),
  person("Jim", "Lemon", role = c("aut", "cph")),
  person("Guillaume", "Louvel", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-7745-0785")),
  person("Federico", "Marotta", role = c("aut", "cph")),
  person("Eric", "Marcon", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-5249-321X")),
  person("Rosemary", "McCloskey", role = c("aut", "cph"), comment = c(ORCID = "0000-0002-9772-8553")),
  person("Johan", "Nylander", role = c("aut", "cph")),
  person("Rainer", "Opgen-Rhein", role = c("aut", "cph")),
  person("Andrei-Alin", "Popescu", role = c("aut", "cph")),
  person("Manuela", "Royer-Carenzi", role = c("aut", "cph")),
  person("Klaus", "Schliep", role = c("aut", "cph"), comment = c(ORCID = "0000-0003-2941-0161")),
  person("Korbinian", "Strimmer", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-7917-2056")),
  person("Damien", "de Vienne", role = c("aut", "cph"), comment = c(ORCID = "0000-0001-9532-5251")))
Depends: R (>= 3.2.0)
Suggests: gee, expm, igraph, knitr, phangorn, xml2
Imports: nlme, lattice, graphics, methods, stats, utils, parallel, Rcpp
        (>= 0.12.0), digest
LinkingTo: Rcpp
VignetteBuilder: utils, knitr
ZipData: no
Description: 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, MAFFT) whose results are
        returned into R.
License: GPL-2 | GPL-3
URL: https://github.com/emmanuelparadis/ape
BugReports: https://github.com/emmanuelparadis/ape/issues
Encoding: UTF-8
Repository: https://phylotastic.r-universe.dev
Date/Publication: 2026-06-17 15:46:37 UTC
RemoteUrl: https://github.com/emmanuelparadis/ape
RemoteRef: HEAD
RemoteSha: 2032ad30eca3e19558bc3a545d47abe2d1f66141
NeedsCompilation: yes
Packaged: 2026-06-23 23:36:33 UTC; root
Author: Emmanuel Paradis [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0003-3092-2199>),
  Simon Blomberg [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-1062-0839>),
  Ben Bolker [aut, cph] (ORCID: <https://orcid.org/0000-0002-2127-0443>),
  Joseph Brown [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-3835-8062>),
  Santiago Claramunt [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-8926-5974>),
  Julien Claude [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-9267-1228>),
  Hoa Sien Cuong [aut, cph],
  Richard Desper [aut, cph],
  Gilles Didier [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-0596-9112>),
  Benoit Durand [aut, cph],
  Julien Dutheil [aut, cph] (ORCID:
    <https://orcid.org/0000-0001-7753-4121>),
  RJ Ewing [aut, cph],
  Olivier Gascuel [aut, cph],
  Thomas Guillerme [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-4325-1275>),
  Christoph Heibl [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-7655-3299>),
  Anthony Ives [aut, cph] (ORCID:
    <https://orcid.org/0000-0001-9375-9523>),
  Bradley Jones [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-4498-1069>),
  Franz Krah [aut, cph] (ORCID: <https://orcid.org/0000-0001-7866-7508>),
  Daniel Lawson [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-5311-6213>),
  Vincent Lefort [aut, cph],
  Pierre Legendre [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-3838-3305>),
  Jim Lemon [aut, cph],
  Guillaume Louvel [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-7745-0785>),
  Federico Marotta [aut, cph],
  Eric Marcon [aut, cph] (ORCID: <https://orcid.org/0000-0002-5249-321X>),
  Rosemary McCloskey [aut, cph] (ORCID:
    <https://orcid.org/0000-0002-9772-8553>),
  Johan Nylander [aut, cph],
  Rainer Opgen-Rhein [aut, cph],
  Andrei-Alin Popescu [aut, cph],
  Manuela Royer-Carenzi [aut, cph],
  Klaus Schliep [aut, cph] (ORCID:
    <https://orcid.org/0000-0003-2941-0161>),
  Korbinian Strimmer [aut, cph] (ORCID:
    <https://orcid.org/0000-0001-7917-2056>),
  Damien de Vienne [aut, cph] (ORCID:
    <https://orcid.org/0000-0001-9532-5251>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>