Package: sitePath
Type: Package
Title: Phylogeny-based sequence clustering with site polymorphism
Version: 1.26.0
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 libfontconfig1-dev libfreetype6-dev
        make libicu-dev libpng-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-10-29 14:51:09 UTC
RemoteUrl: https://github.com/bioc/sitePath
RemoteRef: RELEASE_3_22
RemoteSha: a93a74d7072e24c9d14e0bcca3884750c9a40306
NeedsCompilation: yes
Packaged: 2026-02-27 08:19:31 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 4.5.2; x86_64-w64-mingw32; 2026-02-27 08:21:25 UTC; windows
Archs: x64
