{
  "_id": "6aca84c6fe5cc25786e8ab9e",
  "Package": "sitePath",
  "Type": "Package",
  "Title": "Phylogeny-based sequence clustering with site polymorphism",
  "Version": "1.29.0",
  "Authors@R": "c(person(\"Chengyang\", \"Ji\",\nemail = \"chengyang.ji12@alumni.xjtlu.edu.cn\",\nrole = c(\"aut\", \"cre\", \"cph\"),\ncomment = c(ORCID = \"0000-0001-9258-5453\")),\nperson(\"Hangyu\", \"Zhou\",\nemail = \"zhy@ism.cams.cn\",\nrole = c(\"ths\")),\nperson(\"Aiping\", \"Wu\",\nemail = \"wap@ism.cams.cn\",\nrole = c(\"ths\")))",
  "Description": "Using site polymorphism is one of the ways to cluster\nDNA/protein sequences but it is possible for the sequences with\nthe same polymorphism on a single site to be genetically\ndistant. This package is aimed at clustering sequences using\nsite polymorphism and their corresponding phylogenetic trees.\nBy considering their location on the tree, only the\nstructurally adjacent sequences will be clustered. However, the\nadjacent sequences may not necessarily have the same\npolymorphism. So a branch-and-bound like algorithm is used to\nminimize the entropy representing the purity of site\npolymorphism of each cluster.",
  "License": "MIT + file LICENSE",
  "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,\nSoftware",
  "Config/pak/sysreqs": "libcairo2-dev cmake libfontconfig1-dev\nlibfreetype6-dev make libicu-dev libpng-dev libuv1-dev\nzlib1g-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": {
    "Date": "2026-10-10 16:57:48 UTC",
    "User": "root"
  },
  "Author": "Chengyang Ji [aut, cre, cph] (ORCID:\n<https://orcid.org/0000-0001-9258-5453>),\nHangyu Zhou [ths],\nAiping Wu [ths]",
  "Maintainer": "Chengyang Ji <chengyang.ji12@alumni.xjtlu.edu.cn>",
  "_user": "bioc",
  "_type": "src",
  "_file": "sitePath_1.29.0.tar.gz",
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  "_filesize": 1189279,
  "_sha256": "8c8078893b9d7dba69f2ce32d9599a5a8574a8d4ed8ffde02e1611823f190df6",
  "_expires": "2027-01-18T18:32:36.000Z",
  "_created": "2026-10-10T16:57:48.000Z",
  "_published": "2026-10-10T18:32:38.710Z",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/38069505600",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_bioccheck": {
    "error": 0,
    "warning": 2,
    "note": 8
  },
  "_upstream": "https://github.com/bioc/sitePath",
  "_commit": {
    "id": "0b270a1503376f9a1311cff564d549934a72525b",
    "author": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "committer": "A Wokaty <andres.wokaty@sph.cuny.edu>",
    "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n",
    "time": 1777380594
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  "_maintainer": {
    "name": "Chengyang Ji",
    "email": "chengyang.ji12@alumni.xjtlu.edu.cn",
    "login": "jichengyang202301",
    "orcid": "0000-0001-9258-5453",
    "description": "I hate coding",
    "uuid": 17981888
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  "_distro": "resolute",
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  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
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  ],
  "_tags": [],
  "_bioc": [
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      "branch": "devel",
      "version": "1.29.0",
      "bioc": "3.24",
      "repository": "bioc"
    },
    {
      "branch": "release",
      "version": "1.28.0",
      "bioc": "3.23",
      "repository": "bioc"
    }
  ],
  "_topics": [
    "alignment",
    "multiplesequencealignment",
    "phylogenetics",
    "snp",
    "software",
    "mutation",
    "cpp"
  ],
  "_stars": 11,
  "_contributors": [
    {
      "user": "jichengyang202301",
      "count": 369,
      "uuid": 17981888
    },
    {
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    "name": "Bioconductor",
    "followers": 476,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 408,
    "source": "https://www.bioconductor.org/packages/stats/bioc/sitePath"
  },
  "_devurl": "https://github.com/wuaipinglab/sitepath",
  "_pkgdown": "https://wuaipinglab.github.io/sitePath/",
  "_searchresults": 10,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/sitePath.html",
    "LICENSE"
  ],
  "_homeurl": "https://github.com/wuaipinglab/sitepath",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "addMSA",
    "allSitesName",
    "as.phylo",
    "as.treedata",
    "extractSite",
    "extractTips",
    "fixationIndels",
    "fixationPath",
    "fixationSites",
    "groupTips",
    "lineagePath",
    "multiFixationSites",
    "paraFixSites",
    "parallelSites",
    "plotFixationSites",
    "plotMutSites",
    "plotParallelSites",
    "plotSingleSite",
    "read.alignment",
    "read.tree",
    "setSiteNumbering",
    "similarityMatrix",
    "sitesMinEntropy",
    "sneakPeek",
    "SNPsites"
  ],
  "_datasets": [
    {
      "name": "h3n2_align",
      "title": "Multiple sequence alignment of H3N2's HA protein",
      "object": "h3n2_align",
      "file": "h3n2_align.rda",
      "class": [
        "alignment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "h3n2_align_reduced",
      "title": "Multiple sequence alignment of H3N2's HA protein",
      "object": "h3n2_align_reduced",
      "file": "h3n2_align_reduced.rda",
      "class": [
        "alignment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "h3n2_tree",
      "title": "Phylogenetic tree of H3N2's HA protein",
      "object": "h3n2_tree",
      "file": "h3n2_tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "h3n2_tree_reduced",
      "title": "Phylogenetic tree of H3N2's HA protein",
      "object": "h3n2_tree_reduced",
      "file": "h3n2_tree_reduced.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sars2_align",
      "title": "Multiple sequence alignment of SARS-CoV-2 genome CDS",
      "object": "sars2_align",
      "file": "sars2_align.rda",
      "class": [
        "alignment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "sars2_tree",
      "title": "Phylogenetic tree of SARS-CoV-2 genome CDS",
      "object": "sars2_tree",
      "file": "sars2_tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "zikv_align",
      "title": "Multiple sequence alignment of Zika virus polyprotein",
      "object": "zikv_align",
      "file": "zikv_align.rda",
      "class": [
        "alignment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "zikv_align_reduced",
      "title": "Multiple sequence alignment of Zika virus polyprotein",
      "object": "zikv_align_reduced",
      "file": "zikv_align_reduced.rda",
      "class": [
        "alignment"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "zikv_tree",
      "title": "Phylogenetic tree of Zika virus polyprotein",
      "object": "zikv_tree",
      "file": "zikv_tree.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "zikv_tree_reduced",
      "title": "Phylogenetic tree of Zika virus polyprotein",
      "object": "zikv_tree_reduced",
      "file": "zikv_tree_reduced.rda",
      "class": [
        "phylo"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "allSitesName",
      "title": "Retrieve position of all the sites",
      "topics": [
        "allSitesName",
        "allSitesName.fixationSites",
        "allSitesName.paraFixSites",
        "allSitesName.parallelSites",
        "allSitesName.sitesMinEntropy",
        "allSitesName.SNPsites"
      ]
    },
    {
      "page": "as.data.frame",
      "title": "Convert results to Data Frame",
      "topics": [
        "as.data.frame.fixationSites",
        "as.data.frame.parallelSites",
        "as.data.frame.SNPsites"
      ]
    },
    {
      "page": "extractSite",
      "title": "Extract tips for a single site",
      "topics": [
        "extractSite",
        "extractSite.fixationSites"
      ]
    },
    {
      "page": "extractTips",
      "title": "Extract grouped tips for a single site",
      "topics": [
        "extractTips",
        "extractTips.fixationSites",
        "extractTips.lineagePath",
        "extractTips.parallelSites",
        "extractTips.sitePara",
        "extractTips.sitePath",
        "extractTips.sitesMinEntropy"
      ]
    },
    {
      "page": "fixationIndels",
      "title": "Fixation indels prediction",
      "topics": [
        "fixationIndels",
        "fixationIndels.sitesMinEntropy"
      ]
    },
    {
      "page": "fixationPath",
      "title": "Accumulation of fixed mutation as a tree",
      "topics": [
        "fixationPath",
        "fixationPath.fixationSites",
        "fixationPath.sitesMinEntropy"
      ]
    },
    {
      "page": "fixationSites",
      "title": "Fixation sites prediction",
      "topics": [
        "fixationSites",
        "fixationSites.lineagePath",
        "fixationSites.paraFixSites",
        "fixationSites.sitesMinEntropy"
      ]
    },
    {
      "page": "groupTips",
      "title": "The grouping of tree tips",
      "topics": [
        "groupTips",
        "groupTips.fixationPath",
        "groupTips.fixationSites",
        "groupTips.lineagePath",
        "groupTips.phyMSAmatched",
        "groupTips.sitesMinEntropy"
      ]
    },
    {
      "page": "h3n2_align",
      "title": "Multiple sequence alignment of H3N2's HA protein",
      "topics": [
        "h3n2_align",
        "h3n2_align_reduced"
      ]
    },
    {
      "page": "h3n2_tree",
      "title": "Phylogenetic tree of H3N2's HA protein",
      "topics": [
        "h3n2_tree",
        "h3n2_tree_reduced"
      ]
    },
    {
      "page": "lineagePath",
      "title": "Resolving lineage paths using SNP",
      "topics": [
        "lineagePath",
        "lineagePath.paraFixSites",
        "lineagePath.phylo",
        "lineagePath.phyMSAmatched",
        "lineagePath.sneakPeekedPaths",
        "lineagePath.treedata",
        "sneakPeek"
      ]
    },
    {
      "page": "paraFixSites",
      "title": "The fixation sites with mutation on parallel lineage",
      "topics": [
        "paraFixSites",
        "paraFixSites.lineagePath",
        "paraFixSites.phylo",
        "paraFixSites.sitesMinEntropy",
        "paraFixSites.treedata"
      ]
    },
    {
      "page": "parallelSites",
      "title": "Mutation across multiple phylogenetic lineages",
      "topics": [
        "parallelSites",
        "parallelSites.lineagePath",
        "parallelSites.paraFixSites",
        "parallelSites.sitesMinEntropy"
      ]
    },
    {
      "page": "addMSA",
      "title": "Add matching sequence alignment to the tree",
      "topics": [
        "addMSA",
        "addMSA.phylo",
        "addMSA.treedata",
        "phyMSAmatched"
      ]
    },
    {
      "page": "plotFunctions",
      "title": "Visualize the results",
      "topics": [
        "plot.fixationIndels",
        "plot.fixationPath",
        "plot.fixationSites",
        "plot.lineagePath",
        "plot.parallelSites",
        "plot.phyMSAmatched",
        "plot.sitePath"
      ]
    },
    {
      "page": "plotFixationSites",
      "title": "Plot the result of fixation sites",
      "topics": [
        "plotFixationSites",
        "plotFixationSites.fixationSites",
        "plotFixationSites.paraFixSites"
      ]
    },
    {
      "page": "plotMutSites",
      "title": "Plot tree and mutation sites",
      "topics": [
        "plotMutSites",
        "plotMutSites.fixationSites",
        "plotMutSites.lineagePath",
        "plotMutSites.paraFixSites",
        "plotMutSites.parallelSites",
        "plotMutSites.SNPsites"
      ]
    },
    {
      "page": "plotParallelSites",
      "title": "Plot the result of fixation sites",
      "topics": [
        "plotParallelSites",
        "plotParallelSites.paraFixSites",
        "plotParallelSites.parallelSites"
      ]
    },
    {
      "page": "plotSingleSite",
      "title": "Color the tree by a single site",
      "topics": [
        "plotSingleSite",
        "plotSingleSite.fixationSites",
        "plotSingleSite.lineagePath",
        "plotSingleSite.parallelSites",
        "plotSingleSite.sitesMinEntropy"
      ]
    },
    {
      "page": "sars2_align",
      "title": "Multiple sequence alignment of SARS-CoV-2 genome CDS",
      "topics": [
        "sars2_align"
      ]
    },
    {
      "page": "sars2_tree",
      "title": "Phylogenetic tree of SARS-CoV-2 genome CDS",
      "topics": [
        "sars2_tree"
      ]
    },
    {
      "page": "setSiteNumbering",
      "title": "Set site numbering to the reference sequence",
      "topics": [
        "setSiteNumbering",
        "setSiteNumbering.phyMSAmatched"
      ]
    },
    {
      "page": "similarityMatrix",
      "title": "Similarity between sequences",
      "topics": [
        "similarityMatrix"
      ]
    },
    {
      "page": "sitePath-deprecated",
      "title": "Deprecated functions in package 'sitePath'",
      "topics": [
        "multiFixationSites",
        "sitePath-deprecated"
      ]
    },
    {
      "page": "sitesMinEntropy",
      "title": "Fixation sites prediction",
      "topics": [
        "sitesMinEntropy",
        "sitesMinEntropy.lineagePath"
      ]
    },
    {
      "page": "SNPsites",
      "title": "Finding sites with variation",
      "topics": [
        "SNPsites",
        "SNPsites.phyMSAmatched"
      ]
    },
    {
      "page": "zikv_align",
      "title": "Multiple sequence alignment of Zika virus polyprotein",
      "topics": [
        "zikv_align",
        "zikv_align_reduced"
      ]
    },
    {
      "page": "zikv_tree",
      "title": "Phylogenetic tree of Zika virus polyprotein",
      "topics": [
        "zikv_tree",
        "zikv_tree_reduced"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/sitePath/raw/HEAD/README.md",
  "_rundeps": [
    "ade4",
    "ape",
    "aplot",
    "base64enc",
    "bslib",
    "cachem",
    "cli",
    "cpp11",
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    "dplyr",
    "evaluate",
    "farver",
    "fastmap",
    "fontawesome",
    "fontBitstreamVera",
    "fontLiberation",
    "fontquiver",
    "fs",
    "gdtools",
    "generics",
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      "title": "Use sitePath to find fixation and parallel sites",
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        "Clustering phylogenetic terminals",
        "Import tree file",
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        "The impact of threshold on resolving lineages",
        "Choose a threshold",
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