{
  "_id": "6a496f75ef9e2ed9366e69bb",
  "Package": "phangorn",
  "Title": "Phylogenetic Reconstruction and Analysis",
  "Version": "2.12.1",
  "Authors@R": "c(person(\"Klaus\", \"Schliep\", role = c(\"aut\", \"cre\"),\nemail = \"klaus.schliep@gmail.com\",\ncomment = c(ORCID = \"0000-0003-2941-0161\")),\nperson(\"Emmanuel\", \"Paradis\", role = \"aut\",\ncomment = c(ORCID = \"0000-0003-3092-2199\")),\nperson(\"Leonardo\", \"de Oliveira Martins\", role = \"aut\",\ncomment = c(ORCID = \"0000-0001-5247-1320\")),\nperson(\"Alastair\", \"Potts\", role = \"aut\"),\nperson(\"Iris\", \"Bardel-Kahr\", role = \"aut\",\ncomment = c(ORCID = \"0000-0002-8950-834X\")),\nperson(\"Tim W.\", \"White\", role = \"ctb\"),\nperson(\"Cyrill\", \"Stachniss\", role = \"ctb\"),\nperson(\"Michelle\", \"Kendall\", role = \"ctb\",\nemail = \"m.kendall@imperial.ac.uk\"),\nperson(\"Keren\", \"Halabi\",  role = \"ctb\"),\nperson(\"Richel\", \"Bilderbeek\",  role = \"ctb\"),\nperson(\"Kristin\", \"Winchell\", role = \"ctb\"),\nperson(\"Liam\", \"Revell\", role = \"ctb\"),\nperson(\"Mike\", \"Gilchrist\", role = \"ctb\"),\nperson(\"Jeremy\", \"Beaulieu\", role = \"ctb\"),\nperson(\"Brian\", \"O'Meara\", role = \"ctb\"),\nperson(\"Long\", \"Qu\", role = \"ctb\"),\nperson(given= \"Joseph\", \"Brown\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-3835-8062\")),\nperson(given=\"Santiago\", \"Claramunt\", role = \"ctb\",\ncomment = c(ORCID = \"0000-0002-8926-5974\")))",
  "Description": "Allows for estimation of phylogenetic trees and networks\nusing Maximum Likelihood, Maximum Parsimony, distance methods\nand Hadamard conjugation (Schliep 2011). Offers methods for\ntree comparison, model selection and visualization of\nphylogenetic networks as described in Schliep et al. (2017).",
  "License": "GPL (>= 2)",
  "URL": "https://github.com/KlausVigo/phangorn,\nhttps://klausvigo.github.io/phangorn/",
  "BugReports": "https://github.com/KlausVigo/phangorn/issues",
  "VignetteBuilder": "knitr, utils",
  "biocViews": "Software, Technology, QualityControl",
  "Encoding": "UTF-8",
  "RoxygenNote": "7.3.2",
  "Language": "en-US",
  "Config/testthat/edition": "3",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-06-23 13:40:28 UTC",
    "User": "root"
  },
  "Author": "Klaus Schliep [aut, cre]\n(<https://orcid.org/0000-0003-2941-0161>), Emmanuel Paradis\n[aut] (<https://orcid.org/0000-0003-3092-2199>), Leonardo de\nOliveira Martins [aut]\n(<https://orcid.org/0000-0001-5247-1320>), Alastair Potts\n[aut], Iris Bardel-Kahr [aut]\n(<https://orcid.org/0000-0002-8950-834X>), Tim W. White [ctb],\nCyrill Stachniss [ctb], Michelle Kendall [ctb], Keren Halabi\n[ctb], Richel Bilderbeek [ctb], Kristin Winchell [ctb], Liam\nRevell [ctb], Mike Gilchrist [ctb], Jeremy Beaulieu [ctb],\nBrian O'Meara [ctb], Long Qu [ctb], Joseph Brown [ctb]\n(<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt\n[ctb] (<https://orcid.org/0000-0002-8926-5974>)",
  "Maintainer": "Klaus Schliep <klaus.schliep@gmail.com>",
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://cran.r-universe.dev",
  "Date/Publication": "2024-09-18 02:56:00 UTC",
  "RemoteUrl": "https://github.com/cran/phangorn",
  "RemoteRef": "HEAD",
  "RemoteSha": "1deb35d9618688613e0947eff6521e3334005f7c",
  "_user": "cran",
  "_type": "src",
  "_file": "phangorn_2.12.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/b1556fbe7b83b4847ac9ac06951e4a4da186ca6d47c2112cbc7e26aea6253542",
  "_filesize": 5226214,
  "_sha256": "b1556fbe7b83b4847ac9ac06951e4a4da186ca6d47c2112cbc7e26aea6253542",
  "_expires": "2026-10-12T20:39:15.000Z",
  "_created": "2026-06-23T13:40:28.000Z",
  "_published": "2026-07-04T20:39:17.081Z",
  "_jobs": [
    {
      "job": 85165225906,
      "time": 574,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7822903194"
    },
    {
      "job": 85165225786,
      "time": 627,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "OK",
      "artifact": "7822927026"
    },
    {
      "job": 85165225918,
      "time": 558,
      "config": "linux-release-arm64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7822895017"
    },
    {
      "job": 85165225938,
      "time": 472,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7822853692"
    },
    {
      "job": 85165225570,
      "time": 767,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7822632089"
    },
    {
      "job": 85165225903,
      "time": 730,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7822975732"
    }
  ],
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/cran/actions/runs/28029765661",
  "_status": "success",
  "_upstream": "https://github.com/cran/phangorn",
  "_commit": {
    "id": "1deb35d9618688613e0947eff6521e3334005f7c",
    "author": "Klaus Schliep <klaus.schliep@gmail.com>",
    "committer": "cran-robot <csardi.gabor+cran@gmail.com>",
    "message": "version 2.12.1\n",
    "time": 1726628160
  },
  "_maintainer": {
    "name": "Klaus Schliep",
    "email": "klaus.schliep@gmail.com",
    "login": "klausvigo",
    "description": "Senior Scientist at TU Graz",
    "uuid": 3372431,
    "orcid": "0000-0003-2941-0161"
  },
  "_distro": "resolute",
  "_registered": true,
  "_dependencies": [
    {
      "package": "ape",
      "version": ">= 5.8",
      "role": "Depends"
    },
    {
      "package": "R",
      "version": ">= 4.1.0",
      "role": "Depends"
    },
    {
      "package": "Rcpp",
      "role": "LinkingTo"
    },
    {
      "package": "digest",
      "role": "Imports"
    },
    {
      "package": "fastmatch",
      "role": "Imports"
    },
    {
      "package": "generics",
      "role": "Imports"
    },
    {
      "package": "graphics",
      "role": "Imports"
    },
    {
      "package": "grDevices",
      "role": "Imports"
    },
    {
      "package": "igraph",
      "version": ">= 1.0",
      "role": "Imports"
    },
    {
      "package": "Matrix",
      "role": "Imports"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "parallel",
      "role": "Imports"
    },
    {
      "package": "quadprog",
      "role": "Imports"
    },
    {
      "package": "Rcpp",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "apex",
      "role": "Suggests"
    },
    {
      "package": "Biostrings",
      "role": "Suggests"
    },
    {
      "package": "ggseqlogo",
      "role": "Suggests"
    },
    {
      "package": "ggplot2",
      "role": "Suggests"
    },
    {
      "package": "knitr",
      "role": "Suggests"
    },
    {
      "package": "magick",
      "role": "Suggests"
    },
    {
      "package": "rgl",
      "role": "Suggests"
    },
    {
      "package": "rmarkdown",
      "role": "Suggests"
    },
    {
      "package": "seqinr",
      "role": "Suggests"
    },
    {
      "package": "testthat",
      "version": ">= 3.0.0",
      "role": "Suggests"
    },
    {
      "package": "tinytest",
      "role": "Suggests"
    },
    {
      "package": "vdiffr",
      "role": "Suggests"
    },
    {
      "package": "xtable",
      "role": "Suggests"
    }
  ],
  "_owner": "cran",
  "_selfowned": false,
  "_usedby": 135,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "software",
    "technology",
    "qualitycontrol",
    "openblas",
    "cpp"
  ],
  "_stars": 0,
  "_contributors": [
    {
      "user": "klausvigo",
      "count": 53,
      "uuid": 3372431
    }
  ],
  "_userbio": {
    "uuid": 6899542,
    "type": "organization",
    "name": "cran",
    "followers": 610,
    "description": "Unofficial read-only mirror of all CRAN R packages"
  },
  "_downloads": {
    "count": 26734,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/phangorn"
  },
  "_mentions": 192,
  "_devurl": "https://github.com/klausvigo/phangorn",
  "_pkgdown": "https://klausvigo.github.io/phangorn/",
  "_searchresults": 3504,
  "_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/phangorn.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/klausvigo/phangorn",
  "_realowner": "klausvigo",
  "_cranurl": false,
  "_releases": [
    {
      "version": "0.0-1",
      "date": "2008-03-25"
    },
    {
      "version": "0.0-2",
      "date": "2008-07-20"
    },
    {
      "version": "0.0-3",
      "date": "2008-10-28"
    },
    {
      "version": "0.0-4",
      "date": "2008-12-22"
    },
    {
      "version": "0.0-5",
      "date": "2009-01-22"
    },
    {
      "version": "0.99-2",
      "date": "2009-07-21"
    },
    {
      "version": "0.99-3",
      "date": "2009-10-30"
    },
    {
      "version": "0.99-4",
      "date": "2009-11-27"
    },
    {
      "version": "0.99-5",
      "date": "2010-01-15"
    },
    {
      "version": "0.99-6",
      "date": "2010-01-27"
    },
    {
      "version": "1.0-0",
      "date": "2010-03-18"
    },
    {
      "version": "1.0-1",
      "date": "2010-04-15"
    },
    {
      "version": "1.0-2",
      "date": "2010-05-16"
    },
    {
      "version": "1.1-0",
      "date": "2010-08-28"
    },
    {
      "version": "1.1-1",
      "date": "2010-09-03"
    },
    {
      "version": "1.1-2",
      "date": "2010-09-21"
    },
    {
      "version": "1.2-0",
      "date": "2010-11-22"
    },
    {
      "version": "1.3-0",
      "date": "2011-01-31"
    },
    {
      "version": "1.3-1",
      "date": "2011-02-14"
    },
    {
      "version": "1.4-0",
      "date": "2011-03-27"
    },
    {
      "version": "1.4-1",
      "date": "2011-06-30"
    },
    {
      "version": "1.5-0",
      "date": "2011-12-10"
    },
    {
      "version": "1.5-1",
      "date": "2011-12-13"
    },
    {
      "version": "1.6-0",
      "date": "2012-04-05"
    },
    {
      "version": "1.6-3",
      "date": "2012-07-01"
    },
    {
      "version": "1.6-4",
      "date": "2012-08-02"
    },
    {
      "version": "1.6-5",
      "date": "2012-10-10"
    },
    {
      "version": "1.7-1",
      "date": "2012-10-30"
    },
    {
      "version": "1.7-4",
      "date": "2013-04-04"
    },
    {
      "version": "1.99-1",
      "date": "2013-08-21"
    },
    {
      "version": "1.99-5",
      "date": "2014-01-02"
    },
    {
      "version": "1.99-7",
      "date": "2014-02-02"
    },
    {
      "version": "1.99-8",
      "date": "2014-10-05"
    },
    {
      "version": "1.99-9",
      "date": "2014-10-09"
    },
    {
      "version": "1.99-11",
      "date": "2014-11-11"
    },
    {
      "version": "1.99-12",
      "date": "2015-02-13"
    },
    {
      "version": "1.99-13",
      "date": "2015-04-07"
    },
    {
      "version": "1.99.14",
      "date": "2015-07-09"
    },
    {
      "version": "2.0.0",
      "date": "2015-12-10"
    },
    {
      "version": "2.0.1",
      "date": "2015-12-14"
    },
    {
      "version": "2.0.2",
      "date": "2016-01-22"
    },
    {
      "version": "2.0.3",
      "date": "2016-04-30"
    },
    {
      "version": "2.0.4",
      "date": "2016-06-21"
    },
    {
      "version": "2.1.1",
      "date": "2016-12-04"
    },
    {
      "version": "2.2.0",
      "date": "2017-04-03"
    },
    {
      "version": "2.3.1",
      "date": "2017-11-01"
    },
    {
      "version": "2.4.0",
      "date": "2018-02-15"
    },
    {
      "version": "2.5.3",
      "date": "2019-03-24"
    },
    {
      "version": "2.5.5",
      "date": "2019-06-19"
    },
    {
      "version": "2.6.2",
      "date": "2021-03-22"
    },
    {
      "version": "2.6.3",
      "date": "2021-04-06"
    },
    {
      "version": "2.7.0",
      "date": "2021-05-03"
    },
    {
      "version": "2.7.1",
      "date": "2021-07-13"
    },
    {
      "version": "2.8.0",
      "date": "2021-11-09"
    },
    {
      "version": "2.8.1",
      "date": "2021-12-15"
    },
    {
      "version": "2.9.0",
      "date": "2022-06-16"
    },
    {
      "version": "2.10.0",
      "date": "2022-09-18"
    },
    {
      "version": "2.11.1",
      "date": "2023-01-23"
    },
    {
      "version": "2.12.1",
      "date": "2024-09-17"
    }
  ],
  "_exports": [
    "acctran",
    "acgt2ry",
    "add_boxplot",
    "add_ci",
    "add_edge_length",
    "add_mutations",
    "add_support",
    "add.tips",
    "addConfidences",
    "addTrivialSplits",
    "AICc",
    "allCircularSplits",
    "allCompat",
    "allDescendants",
    "allSitePattern",
    "allSplits",
    "allTrees",
    "anc_pars",
    "anc_pml",
    "Ancestors",
    "ancestral.pars",
    "ancestral.pml",
    "as.ancestral",
    "as.Matrix",
    "as.MultipleAlignment",
    "as.networx",
    "as.phyDat",
    "as.pml",
    "as.splits",
    "as.StringSet",
    "bab",
    "baseFreq",
    "bootstrap.phyDat",
    "bootstrap.pml",
    "c.phyDat",
    "candidate_tree",
    "cbind.phyDat",
    "Children",
    "CI",
    "cladePar",
    "coalSpeciesTree",
    "codon2dna",
    "codonTest",
    "compatible",
    "composition_test",
    "consensusNet",
    "coords",
    "createLabel",
    "delta.score",
    "densiTree",
    "Descendants",
    "designSplits",
    "designTree",
    "dfactorial",
    "discrete.beta",
    "discrete.gamma",
    "dist.hamming",
    "dist.logDet",
    "dist.ml",
    "dist.p",
    "distanceHadamard",
    "distinct.splits",
    "diversity",
    "dna2aa",
    "dna2codon",
    "edQt",
    "fhm",
    "fitch",
    "gap_as_ambiguous",
    "gap_as_state",
    "genlight2phyDat",
    "getClans",
    "getClips",
    "getDiversity",
    "getRoot",
    "getSlices",
    "glance",
    "h2st",
    "h4st",
    "hadamard",
    "has_gap_state",
    "hash",
    "keep_as_tip",
    "KF.dist",
    "latag2n.phyDat",
    "ldfactorial",
    "lento",
    "lli",
    "map_duplicates",
    "mast",
    "matchSplits",
    "maxCladeCred",
    "mcc",
    "midpoint",
    "modelTest",
    "mrca.phylo",
    "multiphyDat2pmlPart",
    "neighborNet",
    "NJ",
    "nni",
    "nnls.networx",
    "nnls.phylo",
    "nnls.splits",
    "nnls.tree",
    "optim.parsimony",
    "optim.pml",
    "pace",
    "parsimony",
    "path.dist",
    "phyDat",
    "phyDat2alignment",
    "phyDat2MultipleAlignment",
    "plot_gamma_plus_inv",
    "plotAnc",
    "plotBS",
    "plotRates",
    "plotSeqLogo",
    "pml",
    "pml_bb",
    "pml.control",
    "pml.fit",
    "pml.free",
    "pml.init",
    "pmlCluster",
    "pmlMix",
    "pmlPart",
    "pmlPart2multiPhylo",
    "pmlPen",
    "pratchet",
    "presenceAbsence",
    "pruneTree",
    "random.addition",
    "ratchet.control",
    "read.nexus.dist",
    "read.nexus.networx",
    "read.nexus.partitions",
    "read.nexus.splits",
    "read.phyDat",
    "readDist",
    "removeAmbiguousSites",
    "removeTrivialSplits",
    "removeUndeterminedSites",
    "RF.dist",
    "RI",
    "rNNI",
    "rSPR",
    "sankoff",
    "SH.test",
    "Siblings",
    "simSeq",
    "SOWH.test",
    "splitsNetwork",
    "SPR.dist",
    "sprdist",
    "superTree",
    "supgma",
    "threshStateC",
    "tidy",
    "transferBootstrap",
    "treedist",
    "UNJ",
    "upgma",
    "wpgma",
    "wRF.dist",
    "write.ancestral",
    "write.nexus.dist",
    "write.nexus.networx",
    "write.nexus.splits",
    "write.phyDat",
    "write.pml",
    "write.splits",
    "writeDist"
  ],
  "_datasets": [
    {
      "name": "chloroplast",
      "title": "Chloroplast alignment",
      "object": "chloroplast",
      "file": "chloroplast.RData",
      "class": [
        "phyDat"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "Laurasiatherian",
      "title": "Laurasiatherian data (AWCMEE)",
      "object": "Laurasiatherian",
      "file": "Laurasiatherian.RData",
      "class": [
        "phyDat"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "mites",
      "title": "Morphological characters of Mites (Schäffer et al. 2010)",
      "object": "mites",
      "file": "mites.RData",
      "class": [
        "phyDat"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    },
    {
      "name": "yeast",
      "title": "Yeast alignment (Rokas et al.)",
      "object": "yeast",
      "file": "yeast.RData",
      "class": [
        "phyDat"
      ],
      "fields": [],
      "table": true,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "parsimony",
      "title": "Parsimony tree.",
      "topics": [
        "acctran",
        "fitch",
        "optim.parsimony",
        "parsimony",
        "pratchet",
        "random.addition",
        "sankoff"
      ]
    },
    {
      "page": "add_ci",
      "title": "Draw Confidences Intervals on Phylogenies",
      "topics": [
        "add_boxplot",
        "add_ci"
      ]
    },
    {
      "page": "add_edge_length",
      "title": "Assign and compute edge lengths from a sample of trees",
      "topics": [
        "add_edge_length"
      ]
    },
    {
      "page": "add.tips",
      "title": "Add tips to a tree",
      "topics": [
        "add.tips"
      ]
    },
    {
      "page": "addConfidences",
      "title": "Compare splits and add support values to an object",
      "topics": [
        "addConfidences",
        "addConfidences.phylo",
        "createLabel",
        "presenceAbsence"
      ]
    },
    {
      "page": "as.splits",
      "title": "Splits representation of graphs and trees.",
      "topics": [
        "addTrivialSplits",
        "allCircularSplits",
        "allSplits",
        "as.bitsplits.splits",
        "as.Matrix",
        "as.Matrix.splits",
        "as.matrix.splits",
        "as.phylo.splits",
        "as.prop.part.splits",
        "as.splits",
        "as.splits.bitsplits",
        "as.splits.multiPhylo",
        "as.splits.networx",
        "as.splits.phylo",
        "c.splits",
        "compatible",
        "distinct.splits",
        "matchSplits",
        "print.splits",
        "removeTrivialSplits",
        "splits",
        "unique.splits"
      ]
    },
    {
      "page": "allTrees",
      "title": "Compute all trees topologies.",
      "topics": [
        "allTrees"
      ]
    },
    {
      "page": "ancestral.pml",
      "title": "Ancestral character reconstruction.",
      "topics": [
        "ancestral.pars",
        "ancestral.pml",
        "anc_pars",
        "anc_pml",
        "as.data.frame.ancestral",
        "as.phyDat.ancestral",
        "pace"
      ]
    },
    {
      "page": "as.networx",
      "title": "Conversion among phylogenetic network objects",
      "topics": [
        "as.networx",
        "as.networx.phylo",
        "as.networx.splits",
        "networx"
      ]
    },
    {
      "page": "pml",
      "title": "Likelihood of a tree.",
      "topics": [
        "anova.pml",
        "as.pml",
        "logLik.pml",
        "optim.pml",
        "pml",
        "print.pml",
        "vcov.pml"
      ]
    },
    {
      "page": "bab",
      "title": "Branch and bound for finding all most parsimonious trees",
      "topics": [
        "bab",
        "BranchAndBound"
      ]
    },
    {
      "page": "baseFreq",
      "title": "Summaries of alignments",
      "topics": [
        "baseFreq",
        "composition_test",
        "glance.phyDat"
      ]
    },
    {
      "page": "bootstrap.pml",
      "title": "Bootstrap",
      "topics": [
        "bootstrap.phyDat",
        "bootstrap.pml"
      ]
    },
    {
      "page": "chloroplast",
      "title": "Chloroplast alignment",
      "topics": [
        "chloroplast"
      ]
    },
    {
      "page": "CI",
      "title": "Consistency Index and Retention Index",
      "topics": [
        "CI",
        "RI"
      ]
    },
    {
      "page": "cladePar",
      "title": "Utility function to plot.phylo",
      "topics": [
        "cladePar"
      ]
    },
    {
      "page": "coalSpeciesTree",
      "title": "Species Tree",
      "topics": [
        "coalSpeciesTree"
      ]
    },
    {
      "page": "codonTest",
      "title": "codonTest",
      "topics": [
        "codonTest"
      ]
    },
    {
      "page": "consensusNet",
      "title": "Computes a consensusNetwork from a list of trees Computes a 'networx' object from a collection of splits.",
      "topics": [
        "consensusNet"
      ]
    },
    {
      "page": "cophenetic.networx",
      "title": "Pairwise Distances from a Phylogenetic Network",
      "topics": [
        "cophenetic.networx",
        "cophenetic.splits"
      ]
    },
    {
      "page": "delta.score",
      "title": "Computes the delta score",
      "topics": [
        "delta.score"
      ]
    },
    {
      "page": "densiTree",
      "title": "Plots a densiTree.",
      "topics": [
        "densiTree"
      ]
    },
    {
      "page": "designTree",
      "title": "Compute a design matrix or non-negative LS",
      "topics": [
        "designSplits",
        "designTree",
        "nnls.networx",
        "nnls.phylo",
        "nnls.splits",
        "nnls.tree"
      ]
    },
    {
      "page": "discrete.gamma",
      "title": "Discrete Gamma and Beta distribution",
      "topics": [
        "discrete.beta",
        "discrete.gamma",
        "plotRates",
        "plot_gamma_plus_inv"
      ]
    },
    {
      "page": "dist.hamming",
      "title": "Pairwise Distances from Sequences",
      "topics": [
        "dist.hamming",
        "dist.logDet",
        "dist.ml"
      ]
    },
    {
      "page": "dist.p",
      "title": "Pairwise Polymorphism P-Distances from DNA Sequences",
      "topics": [
        "dist.p"
      ]
    },
    {
      "page": "distanceHadamard",
      "title": "Distance Hadamard",
      "topics": [
        "distanceHadamard"
      ]
    },
    {
      "page": "dna2codon",
      "title": "Translate nucleic acid sequences into codons",
      "topics": [
        "codon2dna",
        "dna2aa",
        "dna2codon"
      ]
    },
    {
      "page": "gap_as_state",
      "title": "Treat gaps as a state",
      "topics": [
        "gap_as_ambiguous",
        "gap_as_state",
        "has_gap_state"
      ]
    },
    {
      "page": "getClans",
      "title": "Clans, slices and clips",
      "topics": [
        "diversity",
        "getClans",
        "getClips",
        "getDiversity",
        "getSlices",
        "summary.clanistics"
      ]
    },
    {
      "page": "midpoint",
      "title": "Tree manipulation",
      "topics": [
        "getRoot",
        "keep_as_tip",
        "midpoint",
        "midpoint.multiPhylo",
        "midpoint.phylo",
        "pruneTree"
      ]
    },
    {
      "page": "hadamard",
      "title": "Hadamard Matrices and Fast Hadamard Multiplication",
      "topics": [
        "fhm",
        "h2st",
        "h4st",
        "hadamard"
      ]
    },
    {
      "page": "identify.networx",
      "title": "Identify splits in a network",
      "topics": [
        "identify.networx"
      ]
    },
    {
      "page": "image.phyDat",
      "title": "Plot of a Sequence Alignment",
      "topics": [
        "image.phyDat"
      ]
    },
    {
      "page": "latag2n.phyDat",
      "title": "Replace leading and trailing alignment gaps with an ambiguous state",
      "topics": [
        "latag2n.phyDat"
      ]
    },
    {
      "page": "Laurasiatherian",
      "title": "Laurasiatherian data (AWCMEE)",
      "topics": [
        "Laurasiatherian"
      ]
    },
    {
      "page": "dfactorial",
      "title": "Arithmetic Operators",
      "topics": [
        "dfactorial",
        "ldfactorial"
      ]
    },
    {
      "page": "lento",
      "title": "Lento plot",
      "topics": [
        "lento"
      ]
    },
    {
      "page": "pml.fit",
      "title": "Internal maximum likelihood functions.",
      "topics": [
        "edQt",
        "lli",
        "pml.fit",
        "pml.free",
        "pml.init"
      ]
    },
    {
      "page": "mast",
      "title": "Maximum agreement subtree",
      "topics": [
        "mast"
      ]
    },
    {
      "page": "maxCladeCred",
      "title": "Maximum clade credibility tree",
      "topics": [
        "allCompat",
        "maxCladeCred",
        "mcc"
      ]
    },
    {
      "page": "mites",
      "title": "Morphological characters of Mites (Schäffer et al. 2010)",
      "topics": [
        "mites"
      ]
    },
    {
      "page": "modelTest",
      "title": "ModelTest",
      "topics": [
        "AICc",
        "modelTest"
      ]
    },
    {
      "page": "pmlPart",
      "title": "Partition model.",
      "topics": [
        "multiphyDat2pmlPart",
        "pmlPart",
        "pmlPart2multiPhylo"
      ]
    },
    {
      "page": "neighborNet",
      "title": "Computes a neighborNet from a distance matrix",
      "topics": [
        "neighborNet"
      ]
    },
    {
      "page": "NJ",
      "title": "Neighbor-Joining",
      "topics": [
        "NJ",
        "UNJ"
      ]
    },
    {
      "page": "nni",
      "title": "Tree rearrangements.",
      "topics": [
        "nni",
        "rNNI",
        "rSPR"
      ]
    },
    {
      "page": "as.phyDat",
      "title": "Conversion among Sequence Formats",
      "topics": [
        "acgt2ry",
        "as.AAbin.phyDat",
        "as.character.phyDat",
        "as.data.frame.phyDat",
        "as.DNAbin.phyDat",
        "as.MultipleAlignment",
        "as.MultipleAlignment.phyDat",
        "as.phyDat",
        "as.phyDat.AAbin",
        "as.phyDat.AAStringSet",
        "as.phyDat.alignment",
        "as.phyDat.character",
        "as.phyDat.data.frame",
        "as.phyDat.DNAbin",
        "as.phyDat.DNAStringSet",
        "as.phyDat.factor",
        "as.phyDat.matrix",
        "as.phyDat.MultipleAlignment",
        "as.StringSet",
        "as.StringSet.phyDat",
        "genlight2phyDat",
        "phyDat",
        "phyDat2alignment",
        "phyDat2MultipleAlignment"
      ]
    },
    {
      "page": "plot.networx",
      "title": "plot phylogenetic networks",
      "topics": [
        "plot.networx"
      ]
    },
    {
      "page": "plot.pml",
      "title": "Plot phylogeny of a pml object",
      "topics": [
        "plot.pml"
      ]
    },
    {
      "page": "plot.ancestral",
      "title": "Plot ancestral character on a tree",
      "topics": [
        "add_mutations",
        "plotAnc",
        "plotSeqLogo"
      ]
    },
    {
      "page": "plotBS",
      "title": "Plotting trees with bootstrap values",
      "topics": [
        "add_support",
        "plotBS"
      ]
    },
    {
      "page": "pml_bb",
      "title": "Likelihood of a tree.",
      "topics": [
        "pml_bb"
      ]
    },
    {
      "page": "pml.control",
      "title": "Auxiliary for Controlling Fitting",
      "topics": [
        "pml.control",
        "ratchet.control"
      ]
    },
    {
      "page": "pmlCluster",
      "title": "Stochastic Partitioning",
      "topics": [
        "pmlCluster"
      ]
    },
    {
      "page": "pmlMix",
      "title": "Phylogenetic mixture model",
      "topics": [
        "pmlMix"
      ]
    },
    {
      "page": "phyDat",
      "title": "Generic functions for class phyDat",
      "topics": [
        "allSitePattern",
        "c.phyDat",
        "cbind.phyDat",
        "print.phyDat",
        "removeAmbiguousSites",
        "removeUndeterminedSites",
        "subset.phyDat",
        "unique.phyDat",
        "[.phyDat"
      ]
    },
    {
      "page": "read.nexus.partitions",
      "title": "Function to import partitioned data from nexus files",
      "topics": [
        "read.nexus.partitions"
      ]
    },
    {
      "page": "read.nexus.splits",
      "title": "Function to import and export splits and networks",
      "topics": [
        "read.nexus.networx",
        "read.nexus.splits",
        "write.nexus.networx",
        "write.nexus.splits",
        "write.splits"
      ]
    },
    {
      "page": "read.phyDat",
      "title": "Import and export sequence alignments",
      "topics": [
        "read.phyDat",
        "write.phyDat"
      ]
    },
    {
      "page": "SH.test",
      "title": "Shimodaira-Hasegawa Test",
      "topics": [
        "SH.test"
      ]
    },
    {
      "page": "simSeq",
      "title": "Simulate sequences.",
      "topics": [
        "simSeq",
        "simSeq.phylo",
        "simSeq.pml"
      ]
    },
    {
      "page": "SOWH.test",
      "title": "Swofford-Olsen-Waddell-Hillis Test",
      "topics": [
        "SOWH.test"
      ]
    },
    {
      "page": "splitsNetwork",
      "title": "Phylogenetic Network",
      "topics": [
        "splitsNetwork"
      ]
    },
    {
      "page": "superTree",
      "title": "Super Tree methods",
      "topics": [
        "superTree"
      ]
    },
    {
      "page": "transferBootstrap",
      "title": "Transfer Bootstrap",
      "topics": [
        "transferBootstrap"
      ]
    },
    {
      "page": "treedist",
      "title": "Distances between trees",
      "topics": [
        "KF.dist",
        "path.dist",
        "RF.dist",
        "SPR.dist",
        "sprdist",
        "treedist",
        "wRF.dist"
      ]
    },
    {
      "page": "upgma",
      "title": "UPGMA, WPGMA and sUPGMA",
      "topics": [
        "supgma",
        "upgma",
        "wpgma"
      ]
    },
    {
      "page": "write.ancestral",
      "title": "Export and convenience functions for ancestral reconstructions",
      "topics": [
        "as.ancestral",
        "print.ancestral",
        "write.ancestral"
      ]
    },
    {
      "page": "write.pml",
      "title": "Export pml objects",
      "topics": [
        "write.pml"
      ]
    },
    {
      "page": "writeDist",
      "title": "Writing and reading distances in phylip and nexus format",
      "topics": [
        "read.nexus.dist",
        "readDist",
        "unique.dist",
        "write.nexus.dist",
        "writeDist"
      ]
    },
    {
      "page": "yeast",
      "title": "Yeast alignment (Rokas et al.)",
      "topics": [
        "yeast"
      ]
    }
  ],
  "_pkglogo": "https://github.com/cran/phangorn/raw/HEAD/man/figures/logo.png",
  "_readme": "https://github.com/cran/phangorn/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "cli",
    "cpp11",
    "digest",
    "fastmatch",
    "generics",
    "glue",
    "igraph",
    "lattice",
    "lifecycle",
    "magrittr",
    "Matrix",
    "nlme",
    "pkgconfig",
    "quadprog",
    "Rcpp",
    "rlang",
    "vctrs"
  ],
  "_sysdeps": [
    {
      "shlib": "libblas",
      "package": "libopenblas0-pthread",
      "source": "openblas",
      "version": "0.3.32+ds-5",
      "name": "openblas",
      "homepage": "https://www.openblas.net/",
      "description": "Optimized BLAS (linear algebra) library (shared lib, pthread)"
    },
    {
      "shlib": "libstdc++",
      "package": "libstdc++6",
      "source": "gcc",
      "version": "16-20260322-1ubuntu1",
      "name": "c++",
      "homepage": "http://gcc.gnu.org/",
      "description": "GNU Standard C++ Library v3"
    }
  ],
  "_vignettes": [
    {
      "source": "Ancestral.Rmd",
      "filename": "Ancestral.html",
      "title": "Ancestral Sequence Reconstruction",
      "author": "Klaus Schliep",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Parsimony reconstructions",
        "Likelihood reconstructions",
        "Fitting for discrete comparative data",
        "Session info",
        "References"
      ],
      "created": "2021-03-22 13:20:03",
      "modified": "2024-09-18 02:56:00",
      "commits": 5
    },
    {
      "source": "Trees.Rmd",
      "filename": "Trees.html",
      "title": "Estimating phylogenetic trees with phangorn",
      "author": "Klaus Schliep, Iris Bardel-Kahr",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "Getting started",
        "Distance based methods",
        "Bootstrap",
        "Parsimony",
        "Branch and bound",
        "Maximum likelihood",
        "Model selection",
        "Conducting a ML tree",
        "Exporting a tree",
        "Molecular dating with a strict clock for ultrametric and tipdated phylogenies",
        "Session info",
        "References"
      ],
      "created": "2021-03-22 13:20:03",
      "modified": "2024-09-18 02:56:00",
      "commits": 8
    },
    {
      "source": "IntertwiningTreesAndNetworks.Rmd",
      "filename": "IntertwiningTreesAndNetworks.html",
      "title": "Intertwining phylogenetic trees and networks: R Example Script",
      "author": "Klaus Schliep, Alastair Potts, David Morrison and Guido Grimm",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Installing R",
        "Installing the phangorn library",
        "Getting started",
        "Set the working directory",
        "Read in the example file datasets:",
        "Viewing the data",
        "Intertwining trees and network functions",
        "1A:",
        "1B:",
        "1C:",
        "Extras...",
        "",
        "Figure 4"
      ],
      "created": "2016-05-01 00:41:57",
      "modified": "2024-09-18 02:56:00",
      "commits": 9
    },
    {
      "source": "AdvancedFeatures.Rmd",
      "filename": "AdvancedFeatures.html",
      "title": "Markov models and transition rate matrices",
      "author": "Klaus Schliep, Iris Bardel-Kahr",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Introduction",
        "User defined data formats",
        "Markov models of character evolution",
        "Estimation of non-standard transition rate matrices",
        "Predefined models for user defined data",
        "Codon substitution models",
        "Session info",
        "References"
      ],
      "created": "2021-03-22 13:20:03",
      "modified": "2024-09-18 02:56:00",
      "commits": 7
    },
    {
      "source": "MLbyHand.Rmd",
      "filename": "MLbyHand.html",
      "title": "Maximum likelihood by hand",
      "author": "Klaus Schliep, Iris Bardel-Kahr",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Maximum likelihood by hand",
        "Model comparison",
        "Bootstrap",
        "Generating trees",
        "Session info",
        "References"
      ],
      "created": "2023-01-23 09:10:02",
      "modified": "2024-09-18 02:56:00",
      "commits": 2
    },
    {
      "source": "Morphological.Rmd",
      "filename": "Morphological.html",
      "title": "Phylogenetic trees from morphological data",
      "author": "Iris Bardel-Kahr, Klaus Schliep",
      "engine": "knitr::rmarkdown",
      "headings": [
        "Load packages",
        "Load data",
        "Parsimony",
        "Branch and bound",
        "Root trees",
        "Plot trees",
        "Consensus tree",
        "Session info",
        "References"
      ],
      "created": "2023-01-23 09:10:02",
      "modified": "2024-09-18 02:56:00",
      "commits": 2
    },
    {
      "source": "Networx.Rmd",
      "filename": "Networx.html",
      "title": "Splits and Networx",
      "author": "Klaus Schliep",
      "engine": "knitr::rmarkdown",
      "headings": [
        "consensusNet",
        "neighborNet",
        "Adding support values",
        "Estimating edge weights (nnls)",
        "Import and export networks, advanced functions for networx objects",
        "Session Information",
        "References"
      ],
      "created": "2015-02-14 00:46:11",
      "modified": "2024-09-18 02:56:00",
      "commits": 9
    }
  ],
  "_score": 11.123151108776781,
  "_indexed": false,
  "_nocasepkg": "phangorn",
  "_universes": [
    "cran"
  ],
  "_indexurl": "https://klausvigo.r-universe.dev/phangorn",
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.12.1",
      "date": "2026-06-23T13:49:38.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "1deb35d9618688613e0947eff6521e3334005f7c",
      "fileid": "https://r2.ropensci.org/d45f4ca037d24755190fd3ff7be2088ce268530699a70955a04096ea8cb8b25a",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28029765661"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "2.12.1",
      "date": "2026-06-23T13:50:10.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "1deb35d9618688613e0947eff6521e3334005f7c",
      "fileid": "https://r2.ropensci.org/64607f352ea283f69f6c69c23755070386241e04fe4f1b9851fdddcf6b115228",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28029765661"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.12.1",
      "date": "2026-06-23T13:49:23.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "1deb35d9618688613e0947eff6521e3334005f7c",
      "fileid": "https://r2.ropensci.org/247f3cdb1856bbbf5d65eed92a17b80a43566552699b1b51bd6ff2ecdd4b7e41",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28029765661"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "2.12.1",
      "date": "2026-06-23T13:47:38.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "1deb35d9618688613e0947eff6521e3334005f7c",
      "fileid": "https://r2.ropensci.org/a5bfa2b9da9b7d49f5a89075ddedd627f09dc3f61c47a4b7965c84826896a392",
      "status": "success",
      "check": "OK",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28029765661"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "2.12.1",
      "date": "2026-06-23T13:53:20.000Z",
      "arch": "emscripten",
      "commit": "1deb35d9618688613e0947eff6521e3334005f7c",
      "fileid": "https://r2.ropensci.org/6d0cf893aaad6c5c05e6b64d0f87f4faf8955010a732baa41d91b59f8863601b",
      "status": "success",
      "buildurl": "https://github.com/r-universe/cran/actions/runs/28029765661"
    }
  ]
}