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  "Title": "Plot Multiple Sequence Alignment using 'ggplot2'",
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  "Authors@R": "c(person(\"Guangchuang\", \"Yu\", email = \"guangchuangyu@gmail.com\", role = c(\"aut\", \"cre\",\"ths\"), comment = c(ORCID = \"0000-0002-6485-8781\")),\nperson(\"Lang\", \"Zhou\",      email = \"nyzhoulang@gmail.com\",    role = \"aut\"),\nperson(\"Shuangbin\", \"Xu\",   email = \"xshuangbin@163.com\",      role = \"ctb\"),\nperson(\"Huina\", \"Huang\",    email = \"1185796994@qq.com\",       role = \"ctb\"))",
  "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.r-universe.dev",
  "Date/Publication": "2026-04-28 12:57:01 UTC",
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  "Author": "Guangchuang Yu [aut, cre, ths] (ORCID:\n<https://orcid.org/0000-0002-6485-8781>),\nLang Zhou [aut],\nShuangbin Xu [ctb],\nHuina Huang [ctb]",
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    "assign_dms",
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    "available_fonts",
    "available_msa",
    "extract_seq",
    "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": "adjust_ally",
      "topics": [
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      ]
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      "title": "assign_dms",
      "topics": [
        "assign_dms"
      ]
    },
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      "title": "List Color Schemes currently available",
      "topics": [
        "available_colors"
      ]
    },
    {
      "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"
      ]
    },
    {
      "page": "geom_msa",
      "title": "geom_msa",
      "topics": [
        "geom_msa"
      ]
    },
    {
      "page": "geom_msaBar",
      "title": "geom_msaBar",
      "topics": [
        "geom_msaBar"
      ]
    },
    {
      "page": "geom_seed",
      "title": "geom_seed",
      "topics": [
        "geom_seed"
      ]
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      "page": "geom_seqlogo",
      "title": "geom_seqlogo",
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      "page": "gghelix",
      "title": "gghelix",
      "topics": [
        "gghelix"
      ]
    },
    {
      "page": "ggmaf",
      "title": "ggmaf",
      "topics": [
        "ggmaf"
      ]
    },
    {
      "page": "ggmsa",
      "title": "ggmsa",
      "topics": [
        "ggmsa"
      ]
    },
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      "page": "ggSeqBundle",
      "title": "ggSeqBundle",
      "topics": [
        "ggSeqBundle"
      ]
    },
    {
      "page": "Gram-negative_AKL.fasta",
      "title": "Gram-negative_AKL",
      "topics": [
        "Gram-negative_AKL.fasta"
      ]
    },
    {
      "page": "Gram-positive_AKL.fasta",
      "title": "Gram-positive_AKL",
      "topics": [
        "Gram-positive_AKL.fasta"
      ]
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      "title": "GVariation",
      "topics": [
        "GVariation"
      ]
    },
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      "page": "LeaderRepeat_All.fa",
      "title": "A sample DNA alignment sequences",
      "topics": [
        "LeaderRepeat_All.fa"
      ]
    },
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      "page": "merge_seq",
      "title": "merge_seq",
      "topics": [
        "merge_seq"
      ]
    },
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      "title": "plot method for SeqDiff object",
      "topics": [
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        "plot,SeqDiff,ANY-method"
      ]
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      "title": "readSSfile",
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      "title": "Rfam",
      "topics": [
        "Rfam"
      ]
    },
    {
      "page": "sample.fasta",
      "title": "A sample data used in ggmsa",
      "topics": [
        "sample.fasta"
      ]
    },
    {
      "page": "seedSample.fa",
      "title": "microRNA data used in ggmsa",
      "topics": [
        "seedSample.fa"
      ]
    },
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      "title": "seqdiff",
      "topics": [
        "seqdiff"
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      "title": "sequence-link-tree",
      "topics": [
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        "show",
        "show,SeqDiff-method"
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      "title": "simplify_hdata",
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      "title": "simplot",
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      "page": "theme_msa",
      "title": "theme_msa",
      "topics": [
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    },
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      "title": "tidy_hdata",
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      "page": "tidy_maf_df",
      "title": "tidy_maf_df",
      "topics": [
        "tidy_maf_df"
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      "page": "tidy_msa",
      "title": "tidy_msa",
      "topics": [
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    },
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      "page": "TP53_genes.xlsx",
      "title": "genome locus",
      "topics": [
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      ]
    },
    {
      "page": "tp53.fa",
      "title": "TP53 MSA",
      "topics": [
        "tp53.fa"
      ]
    },
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      "page": "treeMSA_plot",
      "title": "treeMSA_plot",
      "topics": [
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