Package: sitePath
Type: Package
Title: Phylogeny-based sequence clustering with site polymorphism
Version: 1.29.0
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
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: 2026-04-28 12:49:54 UTC
RemoteUrl: https://github.com/bioc/sitePath
RemoteRef: HEAD
RemoteSha: 0b270a1503376f9a1311cff564d549934a72525b
NeedsCompilation: yes
Packaged: 2026-05-30 09:50:19 UTC; root
Author: Chengyang Ji [aut, cre, cph] (ORCID:
    <https://orcid.org/0000-0001-9258-5453>),
  Hangyu Zhou [ths],
  Aiping Wu [ths]
Maintainer: Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>
Built: R 4.6.0; x86_64-w64-mingw32; 2026-05-30 10:31:56 UTC; windows
Archs: x64
