DESCRIPTION

Package: sitePath
Type: Package
Title: Phylogeny-based sequence clustering with site polymorphism
Version: 1.13.0
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: Using site polymorphism is one of the ways to cluster DNA/protein
    sequences but it is possible for the sequences with the same polymorphism on
    a single site to be genetically distant. This package is aimed at clustering
    sequences using site polymorphism and their corresponding phylogenetic
    trees. By considering their location on the tree, only the structurally
    adjacent sequences will be clustered. However, the adjacent sequences may
    not necessarily have the same polymorphism. So a branch-and-bound like
    algorithm is used to minimize the entropy representing the purity of site
    polymorphism of each cluster.
License: MIT + file LICENSE
Depends:
    R (>= 4.2)
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: 7.2.1
Encoding: UTF-8
VignetteBuilder: knitr
URL: https://wuaipinglab.github.io/sitePath/
BugReports: https://github.com/wuaipinglab/sitePath/issues
biocViews: Alignment, MultipleSequenceAlignment, Phylogenetics, SNP, Software