Package: ggmsa
Title: Plot Multiple Sequence Alignment using 'ggplot2'
Version: 1.17.0
Authors@R: c(person("Guangchuang", "Yu", email = "guangchuangyu@gmail.com", role = c("aut", "cre","ths"), comment = c(ORCID = "0000-0002-6485-8781")),
             person("Lang", "Zhou",      email = "nyzhoulang@gmail.com",    role = "aut"),
             person("Shuangbin", "Xu",   email = "xshuangbin@163.com",      role = "ctb"),
             person("Huina", "Huang",    email = "1185796994@qq.com",       role = "ctb"))
Description: A visual exploration tool for multiple sequence alignment
        and associated data. Supports MSA of DNA, RNA, and protein
        sequences using 'ggplot2'. Multiple sequence alignment can
        easily be combined with other 'ggplot2' plots, such as
        phylogenetic tree Visualized by 'ggtree', boxplot, genome map
        and so on. More features: visualization of sequence logos,
        sequence bundles, RNA secondary structures and detection of
        sequence recombinations.
Depends: R (>= 4.1.0)
Imports: Biostrings, ggplot2, magrittr, tidyr, utils, stats, aplot,
        RColorBrewer, ggfun (>= 0.2.0), ggforce, dplyr, R4RNA,
        grDevices, seqmagick, grid, methods, ggtree (>= 1.17.1)
Suggests: ggtreeExtra, ape, cowplot, knitr, rmarkdown, readxl,
        ggnewscale, kableExtra, gggenes, statebins, prettydoc, testthat
        (>= 3.0.0), yulab.utils
License: Artistic-2.0
Encoding: UTF-8
URL: https://doi.org/10.1093/bib/bbac222(paper),
        https://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/
        (book)
BugReports: https://github.com/YuLab-SMU/ggmsa/issues
biocViews: Software, Visualization, Alignment, Annotation,
        MultipleSequenceAlignment
RoxygenNote: 7.3.2
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/pak/sysreqs: libcairo2-dev libfontconfig1-dev libfreetype6-dev
        make libicu-dev libpng-dev zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2025-10-29 15:12:22 UTC
RemoteUrl: https://github.com/bioc/ggmsa
RemoteRef: HEAD
RemoteSha: aa847fd0976bf5ae516973519b2e88647f6c2b1e
NeedsCompilation: no
Packaged: 2026-02-02 08:45:24 UTC; root
Author: Guangchuang Yu [aut, cre, ths] (ORCID:
    <https://orcid.org/0000-0002-6485-8781>),
  Lang Zhou [aut],
  Shuangbin Xu [ctb],
  Huina Huang [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Built: R 4.6.0; ; 2026-02-02 08:51:56 UTC; unix
