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DESCRIPTION
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DESCRIPTION
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Package: phangorn
Title: Phylogenetic Reconstruction and Analysis
Version: 3.0.0.0
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:
digest,
fastmatch,
generics,
ggseqlogo,
ggplot2,
graphics,
grDevices,
igraph (>= 1.0),
Matrix,
methods,
parallel,
quadprog,
Rcpp,
stats,
utils
Suggests:
apex,
Biostrings,
knitr,
magick,
rgl,
rmarkdown,
seqinr,
testthat (>= 3.0.0),
tinytest,
vdiffr,
xtable
LinkingTo:
Rcpp
Remotes: github::EmmanuelParadis/ape
VignetteBuilder:
knitr,
utils
biocViews: Software, Technology, QualityControl
Encoding: UTF-8
Repository: CRAN
Roxygen: list(old_usage = TRUE)
RoxygenNote: 7.3.1
Language: en-US
Config/testthat/edition: 3