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  "Title": "Plot Multiple Sequence Alignment using 'ggplot2'",
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  "Description": "A visual exploration tool for multiple sequence alignment\nand associated data. Supports MSA of DNA, RNA, and protein\nsequences using 'ggplot2'. Multiple sequence alignment can\neasily be combined with other 'ggplot2' plots, such as\nphylogenetic tree Visualized by 'ggtree', boxplot, genome map\nand so on. More features: visualization of sequence logos,\nsequence bundles, RNA secondary structures and detection of\nsequence recombinations.",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "URL": "https://doi.org/10.1093/bib/bbac222(paper),\nhttps://www.amazon.com/Integration-Manipulation-Visualization-Phylogenetic-Computational-ebook/dp/B0B5NLZR1Z/\n(book)",
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  "Repository": "https://bioc-release.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:01 UTC",
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    "assign_dms",
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    "available_msa",
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    "facet_msa",
    "geom_GC",
    "geom_helix",
    "geom_msa",
    "geom_msaBar",
    "geom_seed",
    "geom_seqlogo",
    "gghelix",
    "ggmaf",
    "ggmsa",
    "ggSeqBundle",
    "merge_seq",
    "plot",
    "read_maf",
    "readSSfile",
    "reset_pos",
    "seqdiff",
    "seqlogo",
    "show",
    "simplify_hdata",
    "simplot",
    "theme_msa",
    "tidy_hdata",
    "tidy_maf_df",
    "tidy_msa",
    "treeMSA_plot"
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      "title": "assign_dms",
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      "title": "List Color Schemes currently available",
      "topics": [
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      ]
    },
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      "page": "available_fonts",
      "title": "List Font Families currently available",
      "topics": [
        "available_fonts"
      ]
    },
    {
      "page": "available_msa",
      "title": "List MSA objects currently available",
      "topics": [
        "available_msa"
      ]
    },
    {
      "page": "extract_seq",
      "title": "extract_seq",
      "topics": [
        "extract_seq"
      ]
    },
    {
      "page": "facet_msa",
      "title": "segment MSA",
      "topics": [
        "facet_msa"
      ]
    },
    {
      "page": "geom_GC",
      "title": "geom_GC",
      "topics": [
        "geom_GC"
      ]
    },
    {
      "page": "geom_helix",
      "title": "geom_helix",
      "topics": [
        "geom_helix"
      ]
    },
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      "page": "geom_msa",
      "title": "geom_msa",
      "topics": [
        "geom_msa"
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    },
    {
      "page": "geom_msaBar",
      "title": "geom_msaBar",
      "topics": [
        "geom_msaBar"
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    },
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      "page": "geom_seed",
      "title": "geom_seed",
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      "title": "geom_seqlogo",
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      "page": "gghelix",
      "title": "gghelix",
      "topics": [
        "gghelix"
      ]
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      "topics": [
        "ggmaf"
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    },
    {
      "page": "ggmsa",
      "title": "ggmsa",
      "topics": [
        "ggmsa"
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      "topics": [
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    },
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      "title": "Gram-negative_AKL",
      "topics": [
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      ]
    },
    {
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      "title": "Gram-positive_AKL",
      "topics": [
        "Gram-positive_AKL.fasta"
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      "title": "GVariation",
      "topics": [
        "GVariation"
      ]
    },
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      "title": "A sample DNA alignment sequences",
      "topics": [
        "LeaderRepeat_All.fa"
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      "title": "merge_seq",
      "topics": [
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      ]
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    {
      "page": "sample.fasta",
      "title": "A sample data used in ggmsa",
      "topics": [
        "sample.fasta"
      ]
    },
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      "page": "seedSample.fa",
      "title": "microRNA data used in ggmsa",
      "topics": [
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      "page": "TP53_genes.xlsx",
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      "page": "tp53.fa",
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