Package: sitePath
Type: Package
Title: Phylogenetic pathway–dependent recognition of fixed substitutions and 
    parallel mutations
Version: 1.8.4
Authors@R: c(person("Chengyang", "Ji",
                    email = "chengyang.ji12@alumni.xjtlu.edu.cn",
                    role = c("aut", "cre", "cph"),
                    comment = c(ORCID = "0000-0001-9258-5453")),
             person("Hangyu", "Zhou",
                    email = "zhy@ism.cams.cn",
                    role = c("ths")),
             person("Aiping", "Wu",
                    email = "wap@ism.cams.cn",
                    role = c("ths")))
Description: The package does hierarchical search for fixation and parallel
    mutations given multiple sequence alignment and phylogenetic tree. The
    package also provides visualization of these mutations on the tree.
License: MIT + file LICENSE
Depends:
    R (>= 4.1)
Imports:
    RColorBrewer,
    Rcpp,
    ape,
    aplot,
    ggplot2,
    ggrepel,
    ggtree,
    graphics,
    grDevices,
    gridExtra,
    methods,
    parallel,
    seqinr,
    stats,
    tidytree,
    utils
Suggests:
    BiocStyle,
    devtools,
    knitr,
    magick,
    rmarkdown,
    testthat
LinkingTo: Rcpp
RoxygenNote: 7.1.1
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://wuaipinglab.github.io/sitePath/
BugReports: https://github.com/wuaipinglab/sitePath/issues
biocViews: Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software