Package: ggmsa
Title: Plot Multiple Sequence Alignment using 'ggplot2'
Version: 1.19.1
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,
        MultipleAlignment, 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
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/roxygen2/version: 8.0.0
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev make libicu-dev libpng-dev libuv1-dev
        zlib1g-dev
Repository: https://bioc.r-universe.dev
Date/Publication: 2026-06-09 03:12:09 UTC
RemoteUrl: https://github.com/bioc/ggmsa
RemoteRef: HEAD
RemoteSha: 804859e2adfefb1a6a52153fdba646c8aff1c6f0
NeedsCompilation: no
Packaged: 2026-06-09 07:47:57 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; ; 2026-06-09 07:49:33 UTC; windows
