{
  "_id": "6a200fdeb401979e73448cbc",
  "Package": "rMSA",
  "Title": "Interface for Popular Multiple Sequence Alignment Tools",
  "Description": "Seamlessly interfaces the Multiple Sequence Alignment\nsoftware packages ClustalW, MAFFT, MUSCLE and Kalign\n(downloaded separately) and provides support to calcualte\ndistances between sequences. This work was partially supported\nby grant no. R21HG005912 from the National Human Genome\nResearch Institute.",
  "Version": "0.99.1",
  "Date": "2024-05-22",
  "Author": "Michael Hahsler, Anurag Nagar",
  "Maintainer": "Michael Hahsler <mhahsler@lyle.smu.edu>",
  "biocViews": "Genetics, Sequencing, Infrastructure, Alignment",
  "SystemRequirements": "ClustalW, Kalign, MAFFT, MUSCLE, boxshade",
  "License": "GPL-3",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://mhahsler.r-universe.dev",
  "Date/Publication": "2024-05-22 14:53:27 UTC",
  "RemoteUrl": "https://github.com/mhahsler/rMSA",
  "RemoteRef": "HEAD",
  "RemoteSha": "4772797ab600332496167a20791f0a26c3b711e3",
  "NeedsCompilation": "no",
  "Packaged": {
    "Date": "2026-06-03 11:25:04 UTC",
    "User": "root"
  },
  "MD5sum": "bfb299ebd8e4fc3d3eb2f9acf24eb33a",
  "_user": "mhahsler",
  "_type": "src",
  "_file": "rMSA_0.99.1.tar.gz",
  "_fileid": "44e5b474d181fbef2c4ac231233fb65822b468147c72f0b67a4a24c9713eb2b1",
  "_filesize": 666034,
  "_sha256": "44e5b474d181fbef2c4ac231233fb65822b468147c72f0b67a4a24c9713eb2b1",
  "_created": "2026-06-03T11:25:04.000Z",
  "_published": "2026-06-03T11:28:30.494Z",
  "_distro": "noble",
  "_jobs": [
    {
      "job": 79282877395,
      "time": 155,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7383269569"
    },
    {
      "job": 79282877343,
      "time": 154,
      "config": "linux-release-x86_64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7383269223"
    },
    {
      "job": 79282877361,
      "time": 135,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7383262860"
    },
    {
      "job": 79282877424,
      "time": 159,
      "config": "macos-release-arm64",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7383270916"
    },
    {
      "job": 79282380120,
      "time": 185,
      "config": "source",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7383216941"
    },
    {
      "job": 79282877497,
      "time": 94,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "7383249037"
    },
    {
      "job": 79282877369,
      "time": 115,
      "config": "windows-devel",
      "r": "4.7.0",
      "check": "ERROR",
      "artifact": "7383255607"
    },
    {
      "job": 79282877394,
      "time": 98,
      "config": "windows-oldrel",
      "r": "4.5.3",
      "check": "ERROR",
      "artifact": "7383250305"
    },
    {
      "job": 79282877456,
      "time": 107,
      "config": "windows-release",
      "r": "4.6.0",
      "check": "ERROR",
      "artifact": "7383253017"
    }
  ],
  "_buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414",
  "_status": "success",
  "_host": "GitHub-Actions",
  "_upstream": "https://github.com/mhahsler/rMSA",
  "_commit": {
    "id": "4772797ab600332496167a20791f0a26c3b711e3",
    "author": "Michael Hahsler <mhahsler@smu.edu>",
    "committer": "Michael Hahsler <mhahsler@smu.edu>",
    "message": "Added grouping.\n",
    "time": 1716389607
  },
  "_maintainer": {
    "name": "Michael Hahsler",
    "email": "mhahsler@lyle.smu.edu",
    "login": "mhahsler",
    "description": "I develop packages for AI, ML, and Data Science.",
    "uuid": 14900595
  },
  "_registered": true,
  "_dependencies": [
    {
      "package": "Biostrings",
      "version": ">= 2.26.2",
      "role": "Depends"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "pwalign",
      "role": "Imports"
    },
    {
      "package": "seqLogo",
      "role": "Imports"
    },
    {
      "package": "proxy",
      "role": "Imports"
    },
    {
      "package": "ape",
      "role": "Imports"
    }
  ],
  "_owner": "mhahsler",
  "_selfowned": true,
  "_usedby": 0,
  "_updates": [],
  "_tags": [],
  "_topics": [
    "genetics",
    "sequencing",
    "infrastructure",
    "alignment",
    "bioinformatics",
    "sequence-alignment"
  ],
  "_stars": 12,
  "_contributors": [
    {
      "user": "mhahsler",
      "count": 27,
      "uuid": 14900595
    },
    {
      "user": "jeanmanguy",
      "count": 1,
      "uuid": 12143588
    }
  ],
  "_userbio": {
    "uuid": 14900595,
    "type": "user",
    "name": "Michael Hahsler",
    "description": "I develop packages for AI, ML, and Data Science."
  },
  "_downloads": {
    "count": 0,
    "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/rMSA"
  },
  "_devurl": "https://github.com/mhahsler/rmsa",
  "_searchresults": 7,
  "_rbuild": "4.6.0",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/readme.html",
    "extra/readme.md",
    "extra/rMSA.html",
    "manual.pdf"
  ],
  "_cranurl": false,
  "_exports": [
    "boxshade",
    "boxshade_help",
    "c2s",
    "clustal",
    "clustal_help",
    "distAlignment",
    "distApe",
    "distCV",
    "distEdit",
    "distFFP",
    "distKMer",
    "distNSV",
    "distSimRank",
    "kalign",
    "kalign_help",
    "mafft",
    "mafft_help",
    "muscle",
    "muscle_help",
    "mutations",
    "plot.DNAMultipleAlignment",
    "plot.DNAStringSet",
    "plot.RNAMultipleAlignment",
    "plot.RNAStringSet",
    "random_sequences",
    "s2c",
    "simRank"
  ],
  "_help": [
    {
      "page": "boxshade",
      "title": "Boxshade: Shading Multiple Aligned Sequences",
      "topics": [
        "box",
        "boxshade",
        "boxshade_help"
      ]
    },
    {
      "page": "clustal",
      "title": "Run Multiple Sequence Alignment (ClustalW) on a Set of Sequences",
      "topics": [
        "clustal",
        "clustal_help"
      ]
    },
    {
      "page": "dist",
      "title": "Calculate Distances between Sets of Sequences",
      "topics": [
        "dist",
        "distAlignment",
        "distApe",
        "distCV",
        "distEdit",
        "distFFP",
        "distKMer",
        "distNSV",
        "distSimRank"
      ]
    },
    {
      "page": "kalign",
      "title": "Multiple Sequence Alignment (Kalign)",
      "topics": [
        "kalign",
        "kalign_help"
      ]
    },
    {
      "page": "mafft",
      "title": "Run Multiple Sequence Alignment (MAFFT) on a Set of Sequences",
      "topics": [
        "mafft",
        "mafft_help"
      ]
    },
    {
      "page": "MUSCLE",
      "title": "Run Multiple Sequence Alignment (MUSCLE) on a Set of Sequences",
      "topics": [
        "muscle",
        "muscle_help"
      ]
    },
    {
      "page": "mutations",
      "title": "Creates Random Mutations of a Sequence",
      "topics": [
        "mutations"
      ]
    },
    {
      "page": "plot",
      "title": "Plot Genetic Sequences and Alignments",
      "topics": [
        "plot",
        "plot.DNAMultipleAlignment",
        "plot.DNAStringSet",
        "plot.RNAMultipleAlignment",
        "plot.RNAStringSet"
      ]
    },
    {
      "page": "random_sequences",
      "title": "Create a Set of Random Sequences",
      "topics": [
        "random_sequences"
      ]
    },
    {
      "page": "simRank",
      "title": "Compute the SimRank Similarity between Sets of Sequences",
      "topics": [
        "simRank"
      ]
    },
    {
      "page": "c2s",
      "title": "Convenience Functions to Convert Strings to Character Vectors",
      "topics": [
        "c2s",
        "s2c"
      ]
    }
  ],
  "_readme": "https://github.com/mhahsler/rMSA/raw/HEAD/README.md",
  "_rundeps": [
    "ape",
    "BiocGenerics",
    "Biostrings",
    "crayon",
    "digest",
    "generics",
    "IRanges",
    "lattice",
    "nlme",
    "proxy",
    "pwalign",
    "Rcpp",
    "S4Vectors",
    "Seqinfo",
    "seqLogo",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "rMSA.Rnw",
      "filename": "rMSA.pdf",
      "title": "Interface to Popular Multiple Sequence Alignment Tools",
      "engine": "utils::Sweave",
      "headings": [],
      "created": "2015-10-06 17:15:25",
      "modified": "2015-10-06 17:15:25",
      "commits": 1
    }
  ],
  "_score": 3.778151250383644,
  "_indexed": true,
  "_nocasepkg": "rmsa",
  "_universes": [
    "mhahsler"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-06-03T11:27:08.000Z",
      "distro": "noble",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "b7c11a0e4ec0999f1c724fccb4c927d13bc719c34db642b6a0b43cf99c3e51c1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.6.0",
      "os": "linux",
      "version": "0.99.1",
      "date": "2026-06-03T11:27:10.000Z",
      "distro": "noble",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "f11f4b7c227176e17829efb91c0e7d0db71211d18f67b33e488d08d735ca964d",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-06-03T11:27:07.000Z",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "10f42fb678cdbb97f05a58c51e5367981f870e0f6c539ba016e8ecb932012223",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.6.0",
      "os": "mac",
      "version": "0.99.1",
      "date": "2026-06-03T11:27:13.000Z",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "31d134be98ea28d2f46d989f57081a935d1b02a73ddd0f8afa8737d23bfa1988",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "0.99.1",
      "date": "2026-06-03T11:27:01.000Z",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "a82375c0838619fab45878b7f5be9f0e02ebe3f9c13e13218f4cec08f3cd62dd",
      "status": "success",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-06-03T11:26:26.000Z",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "cd9607b4452cad7f0da65e4560b49783ff2c1fc777f21f14ed3504af5ef58487",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-06-03T11:26:11.000Z",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "7836299cf453b87ea0bdab7de0a2c8e552eab5d835fcf457cb6533c6022c57f1",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    },
    {
      "r": "4.6.0",
      "os": "win",
      "version": "0.99.1",
      "date": "2026-06-03T11:26:19.000Z",
      "commit": "4772797ab600332496167a20791f0a26c3b711e3",
      "fileid": "ff608b801224b3584edb2cff1b42b1bad3c974a58c7b5415988e60b666ee3331",
      "status": "failure",
      "check": "ERROR",
      "buildurl": "https://github.com/r-universe/mhahsler/actions/runs/26881461414"
    }
  ]
}