{
  "_id": "6a27a9a424555f66ed533c50",
  "Package": "treeio",
  "Title": "Base Classes and Functions for Phylogenetic Tree Input and\nOutput",
  "Version": "1.36.1",
  "Authors@R": "c(\nperson(\"Guangchuang\", \"Yu\",     email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\"), comment = c(ORCID = \"0000-0002-6485-8781\")),\nperson(\"Tommy Tsan-Yuk\", \"Lam\", email = \"tylam.tommy@gmail.com\",   role = c(\"ctb\", \"ths\")),\nperson(\"Shuangbin\", \"Xu\",       email = \"xshuangbin@163.com\",      role = \"ctb\",           comment = c(ORCID=\"0000-0003-3513-5362\")),\nperson(\"Bradley\", \"Jones\",      email = \"brj1@sfu.ca\",             role = \"ctb\"),\nperson(\"Casey\", \"Dunn\",         email = \"casey_dunn@brown.edu\",    role = \"ctb\"),\nperson(\"Tyler\", \"Bradley\",      email = \"tcb85@drexel.edu\",        role = \"ctb\"),\nperson(\"Konstantinos\", \"Geles\", email = \"konstantinos.geles@studenti.unicz.it\", role = \"ctb\")\n)",
  "Description": "'treeio' is an R package to make it easier to import and\nstore phylogenetic tree with associated data; and to link\nexternal data from different sources to phylogeny. It also\nsupports exporting phylogenetic tree with heterogeneous\nassociated data to a single tree file and can be served as a\nplatform for merging tree with associated data and converting\nfile formats.",
  "VignetteBuilder": "knitr",
  "ByteCompile": "true",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "URL": "https://yulab-smu.top/contribution-tree-data/",
  "BugReports": "https://github.com/YuLab-SMU/treeio/issues",
  "biocViews": "Software, Annotation, Clustering, DataImport,\nDataRepresentation, Alignment, MultipleSequenceAlignment,\nPhylogenetics",
  "RoxygenNote": "7.3.2",
  "Config/pak/sysreqs": "cmake make libicu-dev libuv1-dev",
  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-30 06:46:13 UTC",
  "RemoteUrl": "https://github.com/bioc/treeio",
  "RemoteRef": "RELEASE_3_23",
  "RemoteSha": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-08 07:06:30 UTC",
    "User": "root"
  },
  "Author": "Guangchuang Yu [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6485-8781>),\nTommy Tsan-Yuk Lam [ctb, ths],\nShuangbin Xu [ctb] (ORCID: <https://orcid.org/0000-0003-3513-5362>),\nBradley Jones [ctb],\nCasey Dunn [ctb],\nTyler Bradley [ctb],\nKonstantinos Geles [ctb]",
  "Maintainer": "Guangchuang Yu <guangchuangyu@gmail.com>",
  "MD5sum": "46363c5e38dc483972fae5cea390ebaa",
  "_user": "bioc-release",
  "_type": "src",
  "_file": "treeio_1.36.1.tar.gz",
  "_fileid": "1f50095ac51d6ab55ee4ddf4bee16c725086e305ecbf6197c6b6b4aab00392d2",
  "_filesize": 824240,
  "_sha256": "1f50095ac51d6ab55ee4ddf4bee16c725086e305ecbf6197c6b6b4aab00392d2",
  "_created": "2026-06-08T07:06:30.000Z",
  "_published": "2026-06-09T05:50:28.913Z",
  "_jobs": [
    {
      "job": 80256647727,
      "time": 177,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7499516115"
    },
    {
      "job": 80256647865,
      "time": 199,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7473612124"
    },
    {
      "job": 80256648051,
      "time": 226,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473619341"
    },
    {
      "job": 80256648009,
      "time": 136,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7473625318"
    },
    {
      "job": 80256648068,
      "time": 151,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473626491"
    },
    {
      "job": 80256647857,
      "time": 246,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473560862"
    },
    {
      "job": 80256648204,
      "time": 137,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473596486"
    },
    {
      "job": 80256648214,
      "time": 157,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7473607217"
    },
    {
      "job": 80256647743,
      "time": 109,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7499502269"
    },
    {
      "job": 80256648040,
      "time": 138,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7473597356"
    }
  ],
  "_bioccheck": {
    "error": 1,
    "warning": 3,
    "note": 12
  },
  "_buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/treeio",
  "_commit": {
    "id": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
    "author": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "committer": "Guangchuang Yu <guangchuangyu@gmail.com>",
    "message": "merge 130\n",
    "time": 1777531573
  },
  "_maintainer": {
    "name": "Guangchuang Yu",
    "email": "guangchuangyu@gmail.com",
    "login": "guangchuangyu",
    "twitter": "@guangchuangyu",
    "description": "Professor of Bioinformatics at Southern Medical University.",
    "uuid": 626539,
    "orcid": "0000-0002-6485-8781"
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "dplyr",
      "role": "Imports"
    },
    {
      "package": "jsonlite",
      "role": "Imports"
    },
    {
      "package": "magrittr",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "rlang",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "tibble",
      "role": "Imports"
    },
    {
      "package": "tidytree",
      "version": ">= 0.4.5",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "yulab.utils",
      "version": ">= 0.1.6",
      "role": "Imports"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "cli",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "ggtree",
      "role": "Suggests"
    },
    {
      "package": "igraph",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "phangorn",
      "role": "Suggests"
    },
    {
      "package": "prettydoc",
      "role": "Suggests"
    },
    {
      "package": "purrr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "role": "Suggests"
    },
    {
      "package": "tidyr",
      "role": "Suggests"
    },
    {
      "package": "vroom",
      "role": "Suggests"
    },
    {
      "package": "xml2",
      "role": "Suggests"
    },
    {
      "package": "yaml",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": false,
  "_usedby": 128,
  "_updates": [
    {
      "week": "2025-44",
      "n": 2
    },
    {
      "week": "2026-18",
      "n": 5
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.37.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.36.1",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "software",
    "annotation",
    "clustering",
    "dataimport",
    "datarepresentation",
    "alignment",
    "multiplesequencealignment",
    "phylogenetics",
    "exporter",
    "parser",
    "phylogenetic-trees"
  ],
  "_stars": 104,
  "_contributors": [
    {
      "user": "guangchuangyu",
      "count": 240,
      "uuid": 626539
    },
    {
      "user": "xiangpin",
      "count": 127,
      "uuid": 17870644
    },
    {
      "user": "jwokaty",
      "count": 16,
      "uuid": 1744257
    },
    {
      "user": "brj1",
      "count": 15,
      "uuid": 10039876
    },
    {
      "user": "nturaga",
      "count": 14,
      "uuid": 2746443
    },
    {
      "user": "simongreenhill",
      "count": 14,
      "uuid": 220169
    },
    {
      "user": "tbradley1013",
      "count": 12,
      "uuid": 23705496
    },
    {
      "user": "clearmind777",
      "count": 3,
      "uuid": 139222736
    },
    {
      "user": "hpages",
      "count": 2,
      "uuid": 8810451
    },
    {
      "user": "heavywatal",
      "count": 2,
      "uuid": 1431267
    },
    {
      "user": "vobencha",
      "count": 2,
      "uuid": 2466173
    },
    {
      "user": "jeroen",
      "count": 1,
      "uuid": 216319
    },
    {
      "user": "link-ny",
      "count": 1,
      "uuid": 4392950
    },
    {
      "user": "maelle",
      "count": 1,
      "uuid": 8360597
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 42007,
    "source": "https://www.bioconductor.org/packages/stats/bioc/treeio"
  },
  "_mentions": 32,
  "_devurl": "https://github.com/yulab-smu/treeio",
  "_searchresults": 2656,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "extra/treeio.html",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/yulab-smu/treeio",
  "_realowner": "ropensci",
  "_cranurl": false,
  "_exports": [
    ".data",
    "%<>%",
    "%>%",
    "ancestor",
    "as_tibble",
    "as.phylo",
    "as.treedata",
    "child",
    "drop.tip",
    "find.hclust",
    "full_join",
    "get.data",
    "get.fields",
    "get.placements",
    "get.tree",
    "get.treetext",
    "getNodeNum",
    "inner_join",
    "is.ggtree",
    "is.rooted",
    "isTip",
    "label_branch_paml",
    "mask",
    "merge_tree",
    "MRCA",
    "Nnode",
    "Nnode2",
    "nodeid",
    "nodelab",
    "Ntip",
    "offspring",
    "parent",
    "raxml2nwk",
    "read.astral",
    "read.beast",
    "read.beast.newick",
    "read.codeml",
    "read.codeml_mlc",
    "read.fasta",
    "read.hyphy",
    "read.hyphy.seq",
    "read.iqtree",
    "read.jplace",
    "read.jtree",
    "read.mcmctree",
    "read.mega",
    "read.mega_tabular",
    "read.mrbayes",
    "read.newick",
    "read.nextstrain.json",
    "read.nexus",
    "read.nhx",
    "read.paml_rst",
    "read.phylip",
    "read.phylip.seq",
    "read.phylip.tree",
    "read.phyloxml",
    "read.r8s",
    "read.raxml",
    "read.tree",
    "read.treeqza",
    "read.treetime",
    "rename_taxa",
    "rescale_tree",
    "root",
    "rootnode",
    "rtree",
    "spt",
    "tibble",
    "treedata",
    "write.beast",
    "write.beast.newick",
    "write.jplace",
    "write.jtree",
    "write.nexus",
    "write.tree"
  ],
  "_help": [
    {
      "page": "as.treedata",
      "title": "as.treedata",
      "topics": [
        "as.treedata.phylo"
      ]
    },
    {
      "page": "find.hclust",
      "title": "find the hierarchical cluster analysis among the nodes of graph based on the length of all the shortest paths in the graph.",
      "topics": [
        "find.hclust"
      ]
    },
    {
      "page": "get-placements",
      "title": "get.placements",
      "topics": [
        "get.placements",
        "get.placements.jplace"
      ]
    },
    {
      "page": "get.tree",
      "title": "get.tree",
      "topics": [
        "get.tree"
      ]
    },
    {
      "page": "get.treetext-methods",
      "title": "get.treetext method",
      "topics": [
        "get.treetext"
      ]
    },
    {
      "page": "getNodeNum",
      "title": "getNodeNum",
      "topics": [
        "getNodeNum",
        "Nnode2"
      ]
    },
    {
      "page": "is.ggtree",
      "title": "is.ggtree",
      "topics": [
        "is.ggtree"
      ]
    },
    {
      "page": "jplace-class",
      "title": "Class \"jplace\" This class stores phylogenetic placements",
      "topics": [
        "jplace-class"
      ]
    },
    {
      "page": "label_branch_paml",
      "title": "label_branch_paml",
      "topics": [
        "label_branch_paml"
      ]
    },
    {
      "page": "mask",
      "title": "mask",
      "topics": [
        "mask"
      ]
    },
    {
      "page": "merge_tree",
      "title": "merge_tree",
      "topics": [
        "merge_tree"
      ]
    },
    {
      "page": "print.treedataList",
      "title": "print",
      "topics": [
        "print.treedataList"
      ]
    },
    {
      "page": "raxml2nwk",
      "title": "raxml2nwk",
      "topics": [
        "raxml2nwk"
      ]
    },
    {
      "page": "read.astral",
      "title": "read.astral",
      "topics": [
        "read.astral"
      ]
    },
    {
      "page": "beast-parser",
      "title": "read.beast",
      "topics": [
        "read.beast",
        "read.beast.newick",
        "read.mega",
        "read.mrbayes"
      ]
    },
    {
      "page": "read.codeml",
      "title": "read.codeml",
      "topics": [
        "read.codeml"
      ]
    },
    {
      "page": "read.codeml_mlc",
      "title": "read.codeml_mlc",
      "topics": [
        "read.codeml_mlc"
      ]
    },
    {
      "page": "read.fasta",
      "title": "read.fasta",
      "topics": [
        "read.fasta"
      ]
    },
    {
      "page": "read.hyphy",
      "title": "read.hyphy",
      "topics": [
        "read.hyphy"
      ]
    },
    {
      "page": "read.hyphy.seq",
      "title": "read.hyphy.seq",
      "topics": [
        "read.hyphy.seq"
      ]
    },
    {
      "page": "read.iqtree",
      "title": "read.iqtree",
      "topics": [
        "read.iqtree"
      ]
    },
    {
      "page": "read.jplace",
      "title": "read.jplace",
      "topics": [
        "read.jplace"
      ]
    },
    {
      "page": "read-jtree",
      "title": "read.jtree",
      "topics": [
        "read.jtree"
      ]
    },
    {
      "page": "read.mcmctree",
      "title": "read.mcmctree",
      "topics": [
        "read.mcmctree"
      ]
    },
    {
      "page": "read.mega_tabular",
      "title": "read.mega_tabular",
      "topics": [
        "read.mega_tabular"
      ]
    },
    {
      "page": "read.newick",
      "title": "read.newick",
      "topics": [
        "read.newick"
      ]
    },
    {
      "page": "read.nextstrain.json",
      "title": "read.nextstrain.json",
      "topics": [
        "read.nextstrain.json"
      ]
    },
    {
      "page": "read.nhx",
      "title": "read.nhx",
      "topics": [
        "read.nhx"
      ]
    },
    {
      "page": "read.paml_rst",
      "title": "read.paml_rst",
      "topics": [
        "read.paml_rst"
      ]
    },
    {
      "page": "read.phylip",
      "title": "read.phylip",
      "topics": [
        "read.phylip"
      ]
    },
    {
      "page": "read.phylip.seq",
      "title": "read.phylip.seq",
      "topics": [
        "read.phylip.seq"
      ]
    },
    {
      "page": "read.phylip.tree",
      "title": "read.phylip.tree",
      "topics": [
        "read.phylip.tree"
      ]
    },
    {
      "page": "read.phyloxml",
      "title": "read.phyloxml",
      "topics": [
        "read.phyloxml"
      ]
    },
    {
      "page": "read.r8s",
      "title": "read.r8s",
      "topics": [
        "read.r8s"
      ]
    },
    {
      "page": "read.raxml",
      "title": "read.raxml",
      "topics": [
        "read.raxml"
      ]
    },
    {
      "page": "read.treeqza",
      "title": "read.treeqza",
      "topics": [
        "read.treeqza"
      ]
    },
    {
      "page": "treetime",
      "title": "read.timetree",
      "topics": [
        "read.timetree",
        "read.treetime"
      ]
    },
    {
      "page": "rename_taxa",
      "title": "rename_taxa",
      "topics": [
        "rename_taxa"
      ]
    },
    {
      "page": "rescale_tree",
      "title": "rescale_tree",
      "topics": [
        "rescale_tree"
      ]
    },
    {
      "page": "spt-methods",
      "title": "spt method",
      "topics": [
        "spt"
      ]
    },
    {
      "page": "write.beast",
      "title": "write.beast",
      "topics": [
        "write.beast"
      ]
    },
    {
      "page": "write.beast.newick",
      "title": "write.beast.newick",
      "topics": [
        "write.beast.newick"
      ]
    },
    {
      "page": "write.jplace",
      "title": "write.jplace",
      "topics": [
        "write.jplace"
      ]
    },
    {
      "page": "write-jtree",
      "title": "write.jtree",
      "topics": [
        "write.jtree"
      ]
    }
  ],
  "_pkglogo": "https://github.com/bioc/treeio/raw/RELEASE_3_23/man/figures/logo.png",
  "_readme": "https://github.com/bioc/treeio/raw/RELEASE_3_23/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "cpp11",
    "digest",
    "dplyr",
    "fs",
    "generics",
    "glue",
    "jsonlite",
    "lattice",
    "lazyeval",
    "lifecycle",
    "magrittr",
    "nlme",
    "pillar",
    "pkgconfig",
    "purrr",
    "R6",
    "rappdirs",
    "Rcpp",
    "rlang",
    "stringi",
    "stringr",
    "tibble",
    "tidyr",
    "tidyselect",
    "tidytree",
    "utf8",
    "vctrs",
    "withr",
    "yulab.utils"
  ],
  "_vignettes": [
    {
      "source": "treeio.Rmd",
      "filename": "treeio.html",
      "title": "treeio: Base Classes and Functions for Phylogenetic Tree Input and Output",
      "author": "Guangchuang Yu School of Basic Medical Sciences, Southern Medical University",
      "engine": "knitr::rmarkdown",
      "headings": [],
      "created": "2016-12-06 15:41:49",
      "modified": "2023-11-29 08:00:34",
      "commits": 6
    }
  ],
  "_score": 14.76285765344948,
  "_indexed": false,
  "_nocasepkg": "treeio",
  "_universes": [
    "bioc-release"
  ],
  "_indexurl": "https://ropensci.r-universe.dev/treeio",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.36.1",
      "date": "2026-06-08T07:09:55.000Z",
      "distro": "noble",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "c1487c308c3a4f857d644528a5a704f534b4496384c0b431723d131d60bd0693",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "1.36.1",
      "date": "2026-06-08T07:10:22.000Z",
      "distro": "noble",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "ef337c3ad633540c8edce0d74cbe97c08239b29c06ab4cae56164b2d5db80d2b",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.36.1",
      "date": "2026-06-08T07:10:45.000Z",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "13e402ce98bbc94c811969a0626e4249a43441ad47a4f3c2df2c1456f369a00e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "1.36.1",
      "date": "2026-06-08T07:10:48.000Z",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "cb0a9457acdaa9098ab91328fc225e3fc7422c9d8ad31f4c6c7aa1f840379f8c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.36.1",
      "date": "2026-06-08T07:09:31.000Z",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "230c02366a951a084ae9bb1023c6d9cc642517c2e581b2cd7f4a4df3c143315c",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.36.1",
      "date": "2026-06-08T07:09:16.000Z",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "ec946deaeeeae4055493f940f8c587e6eecd8958cbb53b50832ce494af0c25b8",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.36.1",
      "date": "2026-06-09T05:48:23.000Z",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "f1d10d39c6daa38cbdd6845ec46fa8229d3f7882f5439b38d2c0131e9177d116",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "1.36.1",
      "date": "2026-06-08T07:08:39.000Z",
      "commit": "098376fd6461b23a97dbe4a91f4e366c3e934db9",
      "fileid": "d31dd0ff4261907bfdd6654c11768c4c5162035d6c241df75cd716cec3830148",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc-release/actions/runs/27121388157"
    }
  ]
}