{
  "_id": "6a1ad1ae1d7bb097a09e2a20",
  "Package": "fastreeR",
  "Type": "Package",
  "Title": "Phylogenetic, Distance and Other Calculations on VCF and Fasta\nFiles",
  "Version": "2.3.0",
  "Backend": "2.7.1",
  "biocViews": "Phylogenetics, Metagenomics, Clustering",
  "Authors@R": "c(person(given = \"Anestis\",\nfamily = \"Gkanogiannis\",\nrole = c(\"aut\", \"cre\"),\nemail = \"anestis@gkanogiannis.com\",\ncomment = c(ORCID = \"0000-0002-6441-0688\"))\n)",
  "Description": "Calculate distances, build phylogenetic trees or perform\nhierarchical clustering between the samples of a VCF or FASTA\nfile. Functions are implemented in Java-11 and called via\nrJava. Parallel implementation that operates directly on the\nVCF or FASTA file for fast execution.",
  "License": "GPL-3",
  "Encoding": "UTF-8",
  "Language": "en-US",
  "SystemRequirements": "Java (>= 11)",
  "RoxygenNote": "7.3.3",
  "URL": "https://github.com/gkanogiannis/fastreeR,\nhttps://github.com/gkanogiannis/BioInfoJava-Utils",
  "BugReports": "https://github.com/gkanogiannis/fastreeR/issues",
  "VignetteBuilder": "knitr",
  "Config/testthat/edition": "3",
  "Config/pak/sysreqs": "make default-jdk libicu-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-04-30 08:06:08 UTC",
  "RemoteUrl": "https://github.com/bioc/fastreeR",
  "RemoteRef": "HEAD",
  "RemoteSha": "a85f8f11a4d49db4d207b4867721c4908ceec168",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-30 08:30:44 UTC",
    "User": "root"
  },
  "Author": "Anestis Gkanogiannis [aut, cre] (ORCID:\n<https://orcid.org/0000-0002-6441-0688>)",
  "Maintainer": "Anestis Gkanogiannis <anestis@gkanogiannis.com>",
  "MD5sum": "9a881e5304266b8b3324174bbfafc67c",
  "_user": "bioc",
  "_type": "src",
  "_file": "fastreeR_2.3.0.tar.gz",
  "_fileid": "6e08d168231a3e80b7913f3f24973a9d15cfe16002c863067f987cccae344845",
  "_filesize": 4063148,
  "_sha256": "6e08d168231a3e80b7913f3f24973a9d15cfe16002c863067f987cccae344845",
  "_created": "2026-05-30T08:30:44.000Z",
  "_published": "2026-05-30T12:01:50.661Z",
  "_jobs": [
    {
      "job": 78636717521,
      "time": 149,
      "config": "bioc-checks",
      "r": "4.6.0",
      "check": "WARNING",
      "artifact": "7306856454"
    },
    {
      "job": 78636717522,
      "time": 219,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306863223"
    },
    {
      "job": 78636717520,
      "time": 213,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306862626"
    },
    {
      "job": 78636717537,
      "time": 102,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7308022286"
    },
    {
      "job": 78636717523,
      "time": 105,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7308022501"
    },
    {
      "job": 78636432601,
      "time": 334,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306841452"
    },
    {
      "job": 78636717528,
      "time": 135,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306855252"
    },
    {
      "job": 78636717541,
      "time": 128,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7306854578"
    },
    {
      "job": 78636717530,
      "time": 87,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "OK",
      "artifact": "7306850321"
    },
    {
      "job": 78636717532,
      "time": 110,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7306852726"
    }
  ],
  "_bioccheck": {
    "error": 0,
    "warning": 1,
    "note": 5
  },
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/bioc/fastreeR",
  "_commit": {
    "id": "a85f8f11a4d49db4d207b4867721c4908ceec168",
    "author": "Anestis Gkanogiannis <ganoyan@gmail.com>",
    "committer": "Anestis Gkanogiannis <ganoyan@gmail.com>",
    "message": "Merge remote-tracking branch 'upstream/devel' into devel\n",
    "time": 1777536368
  },
  "_maintainer": {
    "name": "Anestis Gkanogiannis",
    "email": "anestis@gkanogiannis.com",
    "login": "gkanogiannis",
    "linkedin": "in/anestis-gkanogiannis",
    "orcid": "0000-0002-6441-0688",
    "description": "Independent Bioinformatics & AI Consultant,\nPhD in Machine Learning\nAthens University of Economics and Business",
    "uuid": 7030248
  },
  "_distro": "noble",
  "_registered": true,
  "_dependencies": [
    {
      "package": "R",
      "version": ">= 4.4",
      "role": "Depends"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "data.table",
      "role": "Imports"
    },
    {
      "package": "dynamicTreeCut",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "R.utils",
      "role": "Imports"
    },
    {
      "package": "rJava",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "stringr",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "BiocFileCache",
      "role": "Suggests"
    },
    {
      "package": "BiocStyle",
      "role": "Suggests"
    },
    {
      "package": "ggtree",
      "role": "Suggests"
    },
    {
      "package": "graphics",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "memuse",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "spelling",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [
    {
      "week": "2025-22",
      "n": 3
    },
    {
      "week": "2025-23",
      "n": 15
    },
    {
      "week": "2025-26",
      "n": 2
    },
    {
      "week": "2025-31",
      "n": 1
    },
    {
      "week": "2025-32",
      "n": 2
    },
    {
      "week": "2025-43",
      "n": 6
    },
    {
      "week": "2025-44",
      "n": 27
    },
    {
      "week": "2026-06",
      "n": 2
    },
    {
      "week": "2026-17",
      "n": 12
    },
    {
      "week": "2026-18",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "2.3.0",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "2.2.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "phylogenetics",
    "metagenomics",
    "clustering",
    "openjdk"
  ],
  "_stars": 31,
  "_contributors": [
    {
      "user": "gkanogiannis",
      "count": 459,
      "uuid": 7030248
    },
    {
      "user": "jwokaty",
      "count": 30,
      "uuid": 1744257
    },
    {
      "user": "nturaga",
      "count": 4,
      "uuid": 2746443
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 353,
    "source": "https://www.bioconductor.org/packages/stats/bioc/fastreeR"
  },
  "_devurl": "https://github.com/gkanogiannis/fastreer",
  "_searchresults": 28,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/fastreeR.html",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/gkanogiannis/fastreer",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "dist2clusters",
    "dist2tree",
    "fasta2dist",
    "tree2clusters",
    "vcf2clusters",
    "vcf2dist",
    "vcf2istats",
    "vcf2tree"
  ],
  "_help": [
    {
      "page": "dist2clusters",
      "title": "Perform Hierarchical Clustering and tree pruning on a distance matrix",
      "topics": [
        "dist2clusters"
      ]
    },
    {
      "page": "dist2tree",
      "title": "Generate phylogenetic tree from samples of a distance matrix",
      "topics": [
        "dist2tree"
      ]
    },
    {
      "page": "fasta2dist",
      "title": "Calculate distances between sequences of a FASTA file",
      "topics": [
        "fasta2dist"
      ]
    },
    {
      "page": "tree2clusters",
      "title": "Perform Hierarchical Clustering and tree pruning on a phylogenetic tree",
      "topics": [
        "tree2clusters"
      ]
    },
    {
      "page": "vcf2clusters",
      "title": "Perform Hierarchical Clustering and tree pruning on samples of VCF file",
      "topics": [
        "vcf2clusters"
      ]
    },
    {
      "page": "vcf2dist",
      "title": "Calculate distances between samples of a VCF file",
      "topics": [
        "vcf2dist"
      ]
    },
    {
      "page": "vcf2istats",
      "title": "Calculate various per sample statistics from a VCF file",
      "topics": [
        "vcf2istats"
      ]
    },
    {
      "page": "vcf2tree",
      "title": "Generate phylogenetic tree from samples of a VCF file",
      "topics": [
        "vcf2tree"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/fastreeR/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "data.table",
    "digest",
    "dynamicTreeCut",
    "glue",
    "lattice",
    "lifecycle",
    "magrittr",
    "nlme",
    "R.methodsS3",
    "R.oo",
    "R.utils",
    "Rcpp",
    "rJava",
    "rlang",
    "stringi",
    "stringr",
    "vctrs"
  ],
  "_sysdeps": [
    {
      "shlib": "libjvm",
      "package": "openjdk-21-jre-headless",
      "headers": "openjdk-21-jre-headless",
      "source": "openjdk",
      "version": "21.0.11+10-1~24.04.2",
      "name": "openjdk",
      "homepage": "https://openjdk.java.net/",
      "description": "OpenJDK Java runtime, using Hotspot JIT (headless)"
    }
  ],
  "_vignettes": [
    {
      "source": "fastreeR_vignette.Rmd",
      "filename": "fastreeR_vignette.html",
      "title": "fastreeR Vignette",
      "author": "Anestis Gkanogiannis",
      "engine": "knitr::rmarkdown",
      "headings": [
        "About fastreeR",
        "Function overview",
        "Compressed VCF input",
        "Installation",
        "Preparation",
        "Allocate RAM and load required libraries",
        "Download sample vcf file",
        "Download sample fasta files",
        "Functions on vcf files",
        "Sample Statistics",
        "Calculate distances from vcf",
        "Histogram of distances",
        "Plot tree from fastreeR::dist2tree",
        "Bootstrapping example",
        "Bootstrap support explained",
        "Interpretation guidance",
        "Reproducibility note",
        "Bootstrap example (small, runnable)",
        "Optional: nicer plotting with ggtree",
        "Command-line examples",
        "JVM / rJava troubleshooting tips",
        "Windowed VCF analysis",
        "Windowed distance matrices",
        "Windowed trees",
        "Plot tree from stats::hclust",
        "Hierarchical Clustering",
        "Functions on fasta files",
        "Calculate distances from fasta",
        "Session Info"
      ],
      "created": "2022-03-19 21:15:24",
      "modified": "2026-04-24 21:54:28",
      "commits": 24
    }
  ],
  "_score": 6.938519725176492,
  "_indexed": true,
  "_nocasepkg": "fastreer",
  "_universes": [
    "bioc",
    "gkanogiannis"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.3.0",
      "date": "2026-05-30T08:34:16.000Z",
      "distro": "noble",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "da5516e9261758fd13018b48cdd8221a6a815b07e75d20dde328372c78bd998a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.3.0",
      "date": "2026-05-30T08:34:08.000Z",
      "distro": "noble",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "561ff68d3122987317890e0516c0e22d03a4c8dba327ab7416eda645cfff7ab5",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "2.3.0",
      "date": "2026-05-30T12:01:13.000Z",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "0c63881aa655b6a48261fa1bd9b44f3aa0bf7b22455b5195f35761f2c1ec843f",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "2.3.0",
      "date": "2026-05-30T12:01:15.000Z",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "90b49b2774fbfeafeb8f0cdda150eee95c636a1ad15da343217eb6bbff212b7c",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.3.0",
      "date": "2026-05-30T08:33:16.000Z",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "810865c7d96f39a9cf2fe653d5cc2892c1ba8197689ddf76af496f585c3a3a77",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "2.3.0",
      "date": "2026-05-30T08:32:19.000Z",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "e0411bd56a8f02959a7178698b682e1c703ab427702132ad958e320c5d0341e4",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "2.3.0",
      "date": "2026-05-30T08:31:56.000Z",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "5575e550338d111a839e0d84eaabf256b86616d1723f658daccd7f62a766b555",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "2.3.0",
      "date": "2026-05-30T08:32:16.000Z",
      "commit": "a85f8f11a4d49db4d207b4867721c4908ceec168",
      "fileid": "e25ddfbef93c9d5e392e9e5293a021ea10cffc8a0fc3a88b918e93f3b627ce0e",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/26679179890"
    }
  ]
}