{
  "_id": "6a103f56acfb0bcc41c9cd4c",
  "Package": "haplotypes",
  "Type": "Package",
  "Title": "Manipulating DNA Sequences and Estimating Unambiguous Haplotype\nNetwork with Statistical Parsimony",
  "Version": "1.1.3.1",
  "Date": "2023-07-12",
  "Author": "Caner Aktas",
  "Maintainer": "Caner Aktas <caktas.aca@gmail.com>",
  "Description": "Provides S4 classes and methods for reading and\nmanipulating aligned DNA sequences, supporting an indel coding\nmethods (only simple indel coding method is available in the\ncurrent version), showing base substitutions and indels,\ncalculating absolute pairwise distances between DNA sequences,\nand collapses identical DNA sequences into haplotypes or\ninferring haplotypes using user provided absolute pairwise\ncharacter difference matrix.  This package also includes S4\nclasses and methods for estimating genealogical relationships\namong haplotypes using statistical parsimony and plotting\nparsimony networks.",
  "License": "GPL-2",
  "URL": "https://cran.r-project.org,\nhttps://biolsystematics.wordpress.com/r/",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-05-11 08:50:40 UTC",
    "User": "root"
  },
  "Config/pak/sysreqs": "libglpk-dev libxml2-dev",
  "Repository": "https://cnrakt.r-universe.dev",
  "Date/Publication": "2023-07-25 06:31:14 UTC",
  "RemoteUrl": "https://github.com/cnrakt/haplotypes",
  "RemoteRef": "HEAD",
  "RemoteSha": "b4bf6e0818bfe7ded6491f87eefabeee395809a4",
  "MD5sum": "9a9943efad9a14ceb436f0b696ab4ceb",
  "_user": "cnrakt",
  "_type": "src",
  "_file": "haplotypes_1.1.3.1.tar.gz",
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  "_created": "2026-05-11T08:50:40.000Z",
  "_published": "2026-05-22T11:34:46.917Z",
  "_distro": "noble",
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  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/cnrakt/haplotypes",
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    "author": "cnrakt <82604970+cnrakt@users.noreply.github.com>",
    "committer": "GitHub <noreply@github.com>",
    "message": "Update README.md",
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  "_maintainer": {
    "name": "Caner Aktas",
    "email": "caktas.aca@gmail.com",
    "login": "cnrakt",
    "uuid": 82604970
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  "_registered": true,
  "_dependencies": [
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "stats",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "network",
      "role": "Imports"
    },
    {
      "package": "sna",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    },
    {
      "package": "phangorn",
      "role": "Imports"
    },
    {
      "package": "plotrix",
      "role": "Imports"
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  ],
  "_owner": "cnrakt",
  "_selfowned": true,
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  "_updates": [],
  "_tags": [],
  "_stars": 1,
  "_contributors": [
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      "count": 33,
      "uuid": 82604970
    }
  ],
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    "type": "user",
    "name": "cnrakt"
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    "count": 375,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/haplotypes"
  },
  "_mentions": 1,
  "_devurl": "https://github.com/cnrakt/haplotypes",
  "_searchresults": 53,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/haplotypes.html",
    "extra/readme.html",
    "extra/readme.md",
    "manual.pdf"
  ],
  "_homeurl": "https://github.com/cnrakt/haplotypes",
  "_realowner": "cnrakt",
  "_cranurl": true,
  "_releases": [
    {
      "version": "1.0",
      "date": "2015-04-26"
    },
    {
      "version": "1.1",
      "date": "2019-03-17"
    },
    {
      "version": "1.1.1",
      "date": "2020-02-20"
    },
    {
      "version": "1.1.2",
      "date": "2020-02-28"
    },
    {
      "version": "1.1.3",
      "date": "2023-06-29"
    },
    {
      "version": "1.1.3.1",
      "date": "2023-07-15"
    },
    {
      "version": "1.1.3.2",
      "date": "2025-10-06"
    }
  ],
  "_exports": [
    "alltest",
    "append",
    "as.data.frame",
    "as.dna",
    "as.DNAbin",
    "as.list",
    "as.matrix",
    "as.network",
    "as.networx",
    "as.phyDat",
    "basecomp",
    "boot.dna",
    "calcclust",
    "clustersG",
    "contr",
    "distance",
    "ext.nodes",
    "fillendgaps",
    "fillna",
    "geodist.corr",
    "grouping",
    "haplo",
    "haplotype",
    "hapreord",
    "has.cycle",
    "homopoly",
    "image",
    "indelcoder",
    "indtest",
    "ncol",
    "nrow",
    "pairnei",
    "pairneidist",
    "pairPhiST",
    "pairPhiSTdist",
    "parsimnet",
    "parsnet",
    "pegas.amova",
    "pielegend",
    "pieplot",
    "plot",
    "polymorp",
    "read.fas",
    "recdistG",
    "remove.gaps",
    "ren.dupli",
    "rownames",
    "rownames<-",
    "show",
    "sic",
    "steplimit",
    "subs",
    "tolower",
    "toupper",
    "tryconnect",
    "tryconnectG",
    "unique",
    "validity",
    "xhaps"
  ],
  "_datasets": [
    {
      "name": "dna.obj",
      "title": "Example DNA sequence data",
      "object": "dna.obj",
      "file": "dna.obj.rda",
      "class": [
        "Dna"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    }
  ],
  "_help": [
    {
      "page": "haplotypes-package",
      "title": "Manipulating DNA Sequences and Estimating Unambiguous Haplotype Network with Statistical Parsimony",
      "topics": [
        "haplotypes-package",
        "haplotypes"
      ]
    },
    {
      "page": "z[-methods",
      "title": "Extract or replace parts of an object of class 'Dna'",
      "topics": [
        "[,Dna,ANY,ANY,ANY-method",
        "[,Dna-method",
        "[-methods",
        "[<-,Dna,ANY,ANY,ANY-method",
        "[<-,Dna-method"
      ]
    },
    {
      "page": "append-methods",
      "title": "Combines two 'Dna' objects",
      "topics": [
        "append,Dna-method",
        "append-methods"
      ]
    },
    {
      "page": "as.data.frame-methods",
      "title": "Coerces a 'Dna' object to a data.frame",
      "topics": [
        "as.data.frame,Dna-method",
        "as.data.frame-methods"
      ]
    },
    {
      "page": "as.dna-methods",
      "title": "Coerces an object to a 'Dna' object",
      "topics": [
        "as.dna",
        "as.dna,character-method",
        "as.dna,data.frame-method",
        "as.dna,DNAbin-method",
        "as.dna,Haplotype-method",
        "as.dna,list-method",
        "as.dna,matrix-method",
        "as.dna,phyDat-method",
        "as.dna-methods"
      ]
    },
    {
      "page": "as.DNAbin-methods",
      "title": "Coerces an object to a 'DNAbin' object",
      "topics": [
        "as.DNAbin",
        "as.DNAbin,Dna-method",
        "as.DNAbin-methods"
      ]
    },
    {
      "page": "as.list-methods",
      "title": "Methods for function 'as.list' in the Package 'haplotypes'",
      "topics": [
        "as.list,Dna-method",
        "as.list,Haplotype-method",
        "as.list,Parsimnet-method",
        "as.list-methods"
      ]
    },
    {
      "page": "as.matrix-methods",
      "title": "Methods for function 'as.matrix' in the Package 'haplotypes'",
      "topics": [
        "as.matrix,Dna-method",
        "as.matrix-methods"
      ]
    },
    {
      "page": "as.network-methods",
      "title": "Coerces an object to a 'network' object",
      "topics": [
        "as.network",
        "as.network,Parsimnet-method",
        "as.network-methods"
      ]
    },
    {
      "page": "as.networx-methods",
      "title": "Coerces an object to a 'networx' object",
      "topics": [
        "as.networx",
        "as.networx,Parsimnet-method",
        "as.networx-methods"
      ]
    },
    {
      "page": "as.numeric-methods",
      "title": "Coerces a 'Dna' object to a numeric matrix",
      "topics": [
        "as.numeric,Dna-method",
        "as.numeric-methods"
      ]
    },
    {
      "page": "as.phyDat-methods",
      "title": "Coerces an object to a 'phyDat' object",
      "topics": [
        "as.phyDat",
        "as.phyDat,Dna-method",
        "as.phyDat-methods"
      ]
    },
    {
      "page": "basecomp-methods",
      "title": "Calculates base composition",
      "topics": [
        "basecomp",
        "basecomp,Dna-method",
        "basecomp-methods"
      ]
    },
    {
      "page": "boot.dna-methods",
      "title": "Generates single bootstrap replicate",
      "topics": [
        "boot.dna",
        "boot.dna,Dna-method",
        "boot.dna-methods"
      ]
    },
    {
      "page": "distance-methods",
      "title": "Calculates absolute pairwise character difference matrix using a 'Dna' object",
      "topics": [
        "distance",
        "distance,Dna-method",
        "distance-methods"
      ]
    },
    {
      "page": "Dna-class",
      "title": "Class '\"Dna\"' in the Package 'haplotypes'",
      "topics": [
        "Dna",
        "Dna-class"
      ]
    },
    {
      "page": "dna.obj",
      "title": "Example DNA sequence data",
      "topics": [
        "dna.obj"
      ]
    },
    {
      "page": "grouping-methods",
      "title": "Groups haplotypes according to the grouping variable (populations, species, etc.)",
      "topics": [
        "grouping",
        "grouping,Haplotype-method",
        "grouping-methods"
      ]
    },
    {
      "page": "Haplotype-class",
      "title": "Class '\"Haplotype\"' in the Package 'haplotypes'",
      "topics": [
        "Haplotype",
        "Haplotype-class"
      ]
    },
    {
      "page": "haplotype-methods",
      "title": "Methods for function 'haplotype' in the package 'haplotypes'",
      "topics": [
        "haplotype",
        "haplotype,dist-method",
        "haplotype,Dna-method",
        "haplotype,matrix-method",
        "haplotype-methods"
      ]
    },
    {
      "page": "hapreord-methods",
      "title": "Reorders haplotypes according to the ordering factor",
      "topics": [
        "hapreord",
        "hapreord,Haplotype-method",
        "hapreord-methods"
      ]
    },
    {
      "page": "homopoly-methods",
      "title": "Provides the list of homoplastic indels and substitutions",
      "topics": [
        "homopoly",
        "homopoly,Dna-method",
        "homopoly-methods"
      ]
    },
    {
      "page": "image-methods",
      "title": "Display DNA Sequence",
      "topics": [
        "image,Dna-method",
        "image-methods"
      ]
    },
    {
      "page": "indelcoder-methods",
      "title": "Codes gaps",
      "topics": [
        "indelcoder",
        "indelcoder,Dna-method",
        "indelcoder-methods"
      ]
    },
    {
      "page": "length-methods",
      "title": "Methods for function 'length' in the package 'haplotypes'",
      "topics": [
        "length,Dna-method",
        "length,Haplotype-method",
        "length,Parsimnet-method",
        "length-methods"
      ]
    },
    {
      "page": "names-methods",
      "title": "Function to get or set names of a 'Dna' object or 'Parsimnet' object",
      "topics": [
        "names,Dna-method",
        "names,Parsimnet-method",
        "names-methods",
        "names<-,Dna-method",
        "names<-,Parsimnet-method",
        "names<--methods"
      ]
    },
    {
      "page": "ncol-methods",
      "title": "Returns the length of the longest DNA sequence",
      "topics": [
        "ncol,Dna-method",
        "ncol-methods"
      ]
    },
    {
      "page": "nrow-methods",
      "title": "Returns the number of DNA sequences",
      "topics": [
        "nrow,Dna-method",
        "nrow-methods"
      ]
    },
    {
      "page": "pairnei-methods",
      "title": "Provides the average number of pairwise Nei's (D) differences between populations",
      "topics": [
        "pairnei",
        "pairnei,dist-method",
        "pairnei,Dna-method",
        "pairnei,matrix-method",
        "pairnei-methods"
      ]
    },
    {
      "page": "pairPhiST-methods",
      "title": "Provides the pairwise PhiST between populations",
      "topics": [
        "pairPhiST",
        "pairPhiST,dist-method",
        "pairPhiST,Dna-method",
        "pairPhiST,matrix-method",
        "pairPhiST-methods"
      ]
    },
    {
      "page": "Parsimnet-class",
      "title": "Class '\"Parsimnet\"' in the Package 'haplotypes'",
      "topics": [
        "Parsimnet",
        "Parsimnet-class"
      ]
    },
    {
      "page": "parsimnet-methods",
      "title": "Estimates gene genealogies using statistical parsimony",
      "topics": [
        "parsimnet",
        "parsimnet,dist-method",
        "parsimnet,Dna-method",
        "parsimnet,matrix-method",
        "parsimnet-methods"
      ]
    },
    {
      "page": "pielegend-methods",
      "title": "Add Legends to Plots",
      "topics": [
        "pielegend",
        "pielegend,Parsimnet,Haplotype-method",
        "pielegend-methods"
      ]
    },
    {
      "page": "pieplot-methods",
      "title": "Plots pie charts on statistical parsimony network",
      "topics": [
        "pieplot",
        "pieplot,Parsimnet,Haplotype-method",
        "pieplot-methods"
      ]
    },
    {
      "page": "plot-methods",
      "title": "Methods for function 'plot' in the package 'haplotypes'",
      "topics": [
        "plot,Parsimnet,missing-method",
        "plot,Parsimnet-method",
        "plot-methods"
      ]
    },
    {
      "page": "polymorp-methods",
      "title": "Displays polymorphic sites (base substitutions and indels) between two sequences",
      "topics": [
        "polymorp",
        "polymorp,Dna-method",
        "polymorp-methods"
      ]
    },
    {
      "page": "range-methods",
      "title": "Returns the minimum and maximum lengths of the DNA sequences",
      "topics": [
        "range,Dna-method",
        "range-methods"
      ]
    },
    {
      "page": "read.fas",
      "title": "Read sequences from a file in FASTA format",
      "topics": [
        "read.fas"
      ]
    },
    {
      "page": "remove.gaps-methods",
      "title": "Removing gaps from 'Dna' object",
      "topics": [
        "remove.gaps",
        "remove.gaps,Dna-method",
        "remove.gaps-methods"
      ]
    },
    {
      "page": "rownames-methods",
      "title": "Retrieve or set the row names",
      "topics": [
        "rownames,Dna-method",
        "rownames,Parsimnet-method",
        "rownames-methods",
        "rownames<-,Dna-method",
        "rownames<-,Parsimnet-method",
        "rownames<--methods"
      ]
    },
    {
      "page": "show-methods",
      "title": "Methods for function 'show' in the package 'haplotypes'",
      "topics": [
        "show,Dna-method",
        "show,Haplotype-method",
        "show,Parsimnet-method",
        "show-methods"
      ]
    },
    {
      "page": "subs-methods",
      "title": "Displays base substitutions",
      "topics": [
        "subs",
        "subs,Dna-method",
        "subs-methods"
      ]
    },
    {
      "page": "tolower-methods",
      "title": "Convert sequence characters from upper to lower case or vice versa",
      "topics": [
        "tolower,Dna-method",
        "tolower-methods",
        "toupper,Dna-method",
        "toupper-methods"
      ]
    },
    {
      "page": "unique-methods",
      "title": "Extract Unique Sequences",
      "topics": [
        "unique,Dna,ANY-method",
        "unique,Dna-method",
        "unique-methods"
      ]
    }
  ],
  "_readme": "https://github.com/cnrakt/haplotypes/raw/HEAD/README.md",
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  "_nocasepkg": "haplotypes",
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