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  "Title": "Phylogenetic Methods for Multiple Gene Data",
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  "Repository": "https://thibautjombart.r-universe.dev",
  "Date/Publication": "2025-07-24 11:58:06 UTC",
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    "description": "Senior Lecturer at Imperial College London. Consultant in outbreak analytics. R geek. Muay Thai enthusiast. Grindcore vocalist."
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    "extra/citation.html",
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    "extra/citation.txt",
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    "getLocusNames",
    "getNumInd",
    "getNumLoci",
    "getNumSequences",
    "getSequenceNames",
    "getSequences",
    "getTree",
    "initialize",
    "multidna2alignment",
    "multidna2genind",
    "multidna2multiphyDat",
    "multiphyDat2alignment",
    "multiphyDat2genind",
    "multiphyDat2multidna",
    "plot",
    "read.multidna",
    "read.multiFASTA",
    "read.multiphyDat",
    "rm.gaps",
    "setLocusNames<-",
    "show"
  ],
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    {
      "page": "subset.multidna",
      "title": "Subset multidna objects",
      "topics": [
        "[,multidna,ANY,ANY,ANY-method",
        "[,multidna-method",
        "[,multiphyDat,ANY,ANY,ANY-method",
        "[,multiphyDat-method",
        "[.multidna",
        "[.multiphyDat"
      ]
    },
    {
      "page": "accessors",
      "title": "multidna Accessors",
      "topics": [
        "accessors",
        "getLocusNames",
        "getLocusNames,multidna",
        "getLocusNames,multidna-method",
        "getLocusNames,multiphyDat",
        "getLocusNames,multiphyDat-method",
        "getNumInd",
        "getNumInd,multidna",
        "getNumInd,multidna-method",
        "getNumInd,multiphyDat",
        "getNumInd,multiphyDat-method",
        "getNumLoci",
        "getNumLoci,multidna",
        "getNumLoci,multidna-method",
        "getNumLoci,multiphyDat",
        "getNumLoci,multiphyDat-method",
        "getNumSequences",
        "getNumSequences,multidna",
        "getNumSequences,multidna-method",
        "getNumSequences,multiphyDat",
        "getNumSequences,multiphyDat-method",
        "getSequenceNames",
        "getSequenceNames,multidna",
        "getSequenceNames,multidna-method",
        "getSequenceNames,multiphyDat",
        "getSequenceNames,multiphyDat-method",
        "getSequences",
        "getSequences,multidna",
        "getSequences,multidna-method",
        "getSequences,multiphyDat",
        "getSequences,multiphyDat-method",
        "setLocusNames<-",
        "setLocusNames<-,multidna",
        "setLocusNames<-,multidna-method",
        "setLocusNames<-,multiphyDat",
        "setLocusNames<-,multiphyDat-method"
      ]
    },
    {
      "page": "add.gaps",
      "title": "Add gap-only sequences for missing data",
      "topics": [
        "add.gaps",
        "add.gaps,multidna-method",
        "add.gaps,multiphyDat-method",
        "add.gaps.generic",
        "add.gaps.multidna",
        "add.gaps.multiphyDat"
      ]
    },
    {
      "page": "concatenate",
      "title": "Concatenate genes into a single matrix",
      "topics": [
        "concatenate",
        "concatenate,multidna-method",
        "concatenate,multiphyDat-method",
        "concatenate.generic",
        "concatenate.multidna",
        "concatenate.multiphyDat"
      ]
    },
    {
      "page": "dist.multidna",
      "title": "Pairwise distances for multiple gene data",
      "topics": [
        "dist.multidna"
      ]
    },
    {
      "page": "getTree",
      "title": "Build phylogenies from multiple gene data",
      "topics": [
        "getTree"
      ]
    },
    {
      "page": "initialize-multidna-method",
      "title": "multidna constructor",
      "topics": [
        "initialize,multidna-method",
        "initialize,multidna-methods",
        "new.multidna"
      ]
    },
    {
      "page": "initialize-multiphyDat-method",
      "title": "multiphyDat constructor",
      "topics": [
        "initialize,multiphyDat-method",
        "initialize,multiphyDat-methods",
        "new.multiphyDat"
      ]
    },
    {
      "page": "multidna",
      "title": "multidna: class for multiple gene data",
      "topics": [
        "data.frameOrNULL",
        "listOrNULL",
        "multidna",
        "multidna-class"
      ]
    },
    {
      "page": "multidna2alignment",
      "title": "Convert from multidna into alignment (seqinr)",
      "topics": [
        "multidna2alignment",
        "multiphyDat2alignment"
      ]
    },
    {
      "page": "multidna2genind",
      "title": "Convert multidna into genind",
      "topics": [
        "multidna2genind",
        "multiphyDat2genind"
      ]
    },
    {
      "page": "multidna2multiphyDat",
      "title": "Conversions between multidna and multiphyDat",
      "topics": [
        "multidna2multiphyDat",
        "multiphyDat2multidna"
      ]
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      "title": "multiphyDat: class for multiple gene data",
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        "multiphyDat-class"
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        "rm.gaps,multiphyDat-method",
        "rm.gaps.generic",
        "rm.gaps.multidna",
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        "show.multidna"
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      "headings": [
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