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  "Title": "A Tool to Associate FASTA Sequences and Features",
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  "Date": "2026-02-13",
  "Authors@R": "person(given = \"Bettina\", family = \"Budeus\", role = c(\"aut\", \"cre\"), email = \"bettina.budeus@stud.uni-due.de\")",
  "Description": "Provides user friendly methods for the identification of\nsequence patterns that are statistically significantly\nassociated with a property of the sequence. For instance,\nSeqFeatR allows to identify viral immune escape mutations for\nhosts of given HLA types. The underlying statistical method is\nFisher's exact test, with appropriate corrections for multiple\ntesting, or Bayes. Patterns may be point mutations or n-tuple\nof mutations. SeqFeatR offers several ways to visualize the\nresults of the statistical analyses, see Budeus (2016)\n<doi:10.1371/journal.pone.0146409>.",
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  "Author": "Bettina Budeus [aut, cre]",
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    "assocpairfeat",
    "assocpoint",
    "assocpointhierarchical",
    "assocpointpair",
    "assoctuple",
    "comparewithancestral",
    "foundereffectfinder",
    "getfreqs",
    "orPlot",
    "qvalues",
    "rewritetuple",
    "SeqFeatR_GUI",
    "smallmanhattan",
    "tartan",
    "visualizepair",
    "visualizepairfeat",
    "volcanoplot"
  ],
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    {
      "page": "assocpair",
      "title": "Finding pairs of alignment positions that jointly mutate",
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        "assocpair"
      ]
    },
    {
      "page": "assocpairfeat",
      "title": "Finding pairs of sequence alignment positions associated with sequence feature.",
      "topics": [
        "assocpairfeat"
      ]
    },
    {
      "page": "assocpoint",
      "title": "Searches for associations of single alignment positions with feature(s)",
      "topics": [
        "assocpoint"
      ]
    },
    {
      "page": "assocpointhierarchical",
      "title": "Searches for associations of single alignment positions with feature(s) with a simple hierarchical model",
      "topics": [
        "assocpointhierarchical"
      ]
    },
    {
      "page": "assocpointpair",
      "title": "Compare results of SeqFeatRs assocpoint with SeqFeatRs assocpair, assocpairfeat",
      "topics": [
        "assocpointpair"
      ]
    },
    {
      "page": "assoctuple",
      "title": "Searches for associations of a tuple of alignment positions with feature(s)",
      "topics": [
        "assoctuple"
      ]
    },
    {
      "page": "comparewithancestral",
      "title": "Compares ancestral sequence with sequence alignment",
      "topics": [
        "comparewithancestral"
      ]
    },
    {
      "page": "foundereffectfinder",
      "title": "Tries to identify a founder effect in results from SeqFeatRs assocpair",
      "topics": [
        "foundereffectfinder"
      ]
    },
    {
      "page": "getfreqs",
      "title": "Get frequencies for amino acids/nucleotides in alignment window (epitope)",
      "topics": [
        "getfreqs"
      ]
    },
    {
      "page": "orPlot",
      "title": "Visualize odds ratios and p-values from SeqFeatRs assocpoint",
      "topics": [
        "orPlot"
      ]
    },
    {
      "page": "q-values",
      "title": "Calculate q-values from p-values",
      "topics": [
        "qvalues"
      ]
    },
    {
      "page": "rewritetuple",
      "title": "Rewrite result from SeqFeatRs assoctuple",
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        "rewritetuple"
      ]
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    {
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      "title": "GUI for SeqFeatR",
      "topics": [
        "SeqFeatR_GUI"
      ]
    },
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      "page": "smallmanhattan",
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      "topics": [
        "smallmanhattan"
      ]
    },
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      "page": "tartan",
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      "topics": [
        "tartan"
      ]
    },
    {
      "page": "visualizepair",
      "title": "Visualize pairs of alignment positions that jointly mutate",
      "topics": [
        "visualizepair"
      ]
    },
    {
      "page": "visualizepairfeat",
      "title": "Visualize pairs of sequence alignment positions associated with sequence feature.",
      "topics": [
        "visualizepairfeat"
      ]
    },
    {
      "page": "volcanoplot",
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