Package: phangorn
Title: Phylogenetic Reconstruction and Analysis
Version: 3.0.0.1
Authors@R: 
    c(person("Klaus", "Schliep", role = c("aut", "cre"),
             email = "klaus.schliep@gmail.com",
             comment = c(ORCID = "0000-0003-2941-0161")),
      person("Emmanuel", "Paradis", role = "aut",
             comment = c(ORCID = "0000-0003-3092-2199")),
      person("Leonardo", "de Oliveira Martins", role = "aut",
             comment = c(ORCID = "0000-0001-5247-1320")),
      person("Alastair", "Potts", role = "aut"),
      person("Iris", "Bardel-Kahr", role = "aut",
             comment = c(ORCID = "0000-0002-8950-834X")),            
      person("Tim W.", "White", role = "ctb"),
      person("Cyrill", "Stachniss", role = "ctb"),
      person("Michelle", "Kendall", role = "ctb",
             email = "m.kendall@imperial.ac.uk"),
      person("Keren", "Halabi",  role = "ctb"),
      person("Richel", "Bilderbeek",  role = "ctb"),
      person("Kristin", "Winchell", role = "ctb"),
      person("Liam", "Revell", role = "ctb"),
      person("Mike", "Gilchrist", role = "ctb"),
      person("Jeremy", "Beaulieu", role = "ctb"),
      person("Brian", "O'Meara", role = "ctb"),
      person("Long", "Qu", role = "ctb"), 
      person(given= "Joseph", "Brown", role = "ctb", 
             comment = c(ORCID = "0000-0002-3835-8062")),
      person(given="Santiago", "Claramunt", role = "ctb", 
             comment = c(ORCID = "0000-0002-8926-5974")))
Description: Allows for estimation of phylogenetic trees and networks
        using Maximum Likelihood, Maximum Parsimony, distance methods
        and Hadamard conjugation (Schliep 2011). Offers methods for
        tree comparison, model selection and visualization of
        phylogenetic networks as described in Schliep et al. (2017).
License: GPL (>= 2)
URL: https://github.com/KlausVigo/phangorn,
        https://klausvigo.github.io/phangorn/
BugReports: https://github.com/KlausVigo/phangorn/issues
Depends: ape (>= 5.8), R (>= 4.1.0)
Imports: checkmate, digest, future.apply, generics, graphics,
        grDevices, igraph (>= 1.0), Matrix, methods, osqp, parallel,
        progressr, Rcpp, stats, utils
Suggests: apex, bibtex, Biostrings, codetools, ggseqlogo, ggplot2,
        knitr, magick, plot3D, rgl, rmarkdown, rsvg, seqinr,
        tinysnapshot (>= 0.2.0), tinytest, xtable
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr, utils
biocViews: Software, Technology, QualityControl
Encoding: UTF-8
Roxygen: list(old_usage = TRUE, markdown = TRUE, roclets = c
        ("namespace", "rd", "srr::srr_stats_roclet"))
Language: en-US
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libglpk-dev make libxml2-dev
Repository: https://klausvigo.r-universe.dev
Date/Publication: 2026-06-22 12:01:52 UTC
RemoteUrl: https://github.com/klausvigo/phangorn
RemoteRef: HEAD
RemoteSha: 64b067b4f4003a3117b0df95bafd3f85e99157e0
NeedsCompilation: yes
Packaged: 2026-06-23 10:38:48 UTC; root
Author: Klaus Schliep [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-2941-0161>),
  Emmanuel Paradis [aut] (ORCID: <https://orcid.org/0000-0003-3092-2199>),
  Leonardo de Oliveira Martins [aut] (ORCID:
    <https://orcid.org/0000-0001-5247-1320>),
  Alastair Potts [aut],
  Iris Bardel-Kahr [aut] (ORCID: <https://orcid.org/0000-0002-8950-834X>),
  Tim W. White [ctb],
  Cyrill Stachniss [ctb],
  Michelle Kendall [ctb],
  Keren Halabi [ctb],
  Richel Bilderbeek [ctb],
  Kristin Winchell [ctb],
  Liam Revell [ctb],
  Mike Gilchrist [ctb],
  Jeremy Beaulieu [ctb],
  Brian O'Meara [ctb],
  Long Qu [ctb],
  Joseph Brown [ctb] (ORCID: <https://orcid.org/0000-0002-3835-8062>),
  Santiago Claramunt [ctb] (ORCID:
    <https://orcid.org/0000-0002-8926-5974>)
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>