Package: phruta
Type: Package
Title: Phylogenetic Reconstruction and Time-dating
Version: 0.1.3
Authors@R: c(person("Cristian", "Roman Palacios", email = "cromanpa@g.ucla.edu",
                  role = c("aut", "cre"),
           comment = c(ORCID = "0000-0003-1696-4886")),
    person(given = "Anna",
          family = "Krystalli",
          role = c("rev")),
    person(given = "Rayna",
          family = "Harris",
          role = c("rev")),
    person(given = "Frederick",
          family = "Boehm",
          role = c("rev"))
           )
URL: https://docs.ropensci.org/phruta/index.html,
        https://github.com/ropensci/phruta,
        https://ropensci.github.io/phruta/
BugReports: https://github.com/ropensci/phruta/issues
Description: The phruta R package is designed to simplify the basic
        phylogenetic pipeline. Specifically, all code is run within the
        same program and data from intermediate steps are saved in
        independent folders. Furthermore, all code is run within the
        same environment which increases the reproducibility of your
        analysis. phruta retrieves gene sequences, combines newly
        downloaded and local gene sequences, and performs sequence
        alignments.
Encoding: UTF-8
LazyData: true
biocViews:
Depends: R (>= 3.5.0)
Imports: rgbif, pbapply, rentrez, taxize, ips, ape, geiger, methods,
        DECIPHER, reutils, foreach, doParallel, doSNOW, Biostrings,
        msa, odseq, XML, Rogue
RoxygenNote: 7.2.0
Suggests: testthat (>= 3.0.0), covr, knitr, markdown, rmarkdown,
        spelling, utf8
VignetteBuilder: knitr
License: MIT + file LICENSE
Config/testthat/edition: 3
Language: en-US
Roxygen: list(markdown = TRUE)
Remotes: cran/reutils, cran/ips
Config/pak/sysreqs: cmake libglpk-dev make libicu-dev libuv1-dev
        libxml2-dev libssl-dev zlib1g-dev
Repository: https://ropensci.r-universe.dev
Date/Publication: 2026-01-17 10:42:09 UTC
RemoteUrl: https://github.com/ropensci/phruta
RemoteRef: main
RemoteSha: 6a18ef79a3daf286e95c55c1aa13415c5637ad68
NeedsCompilation: no
Packaged: 2026-07-01 08:18:08 UTC; root
Author: Cristian Roman Palacios [aut, cre] (ORCID:
    <https://orcid.org/0000-0003-1696-4886>),
  Anna Krystalli [rev],
  Rayna Harris [rev],
  Frederick Boehm [rev]
Maintainer: Cristian Roman Palacios <cromanpa@g.ucla.edu>