{
  "_id": "6abb76f799f7aa8c6aa446f9",
  "Package": "pwalign",
  "Title": "Perform pairwise sequence alignments",
  "Description": "The two main functions in the package are\npairwiseAlignment() and stringDist(). The former solves\n(Needleman-Wunsch) global alignment, (Smith-Waterman) local\nalignment, and (ends-free) overlap alignment problems. The\nlatter computes the Levenshtein edit distance or pairwise\nalignment score matrix for a set of strings.",
  "biocViews": "Alignment, SequenceMatching, Sequencing, Genetics",
  "URL": "https://bioconductor.org/packages/pwalign",
  "BugReports": "https://github.com/Bioconductor/pwalign/issues",
  "Version": "1.9.1",
  "License": "Artistic-2.0",
  "Encoding": "UTF-8",
  "Authors@R": "c(\nperson(\"Patrick\", \"Aboyoun\", role=\"aut\"),\nperson(\"Robert\", \"Gentleman\", role=\"aut\"),\nperson(\"Hervé\", \"Pagès\", role=\"cre\",\nemail=\"hpages.on.github@gmail.com\",\ncomment=c(ORCID=\"0009-0002-8272-4522\")))",
  "Collate": "00datacache.R utils.R InDel-class.R AlignedXStringSet-class.R\nPairwiseAlignments-class.R\nPairwiseAlignmentsSingleSubject-class.R PairwiseAlignments-io.R\nalign-utils.R pid.R substitution_matrices.R pairwiseAlignment.R\nstringDist.R zzz.R",
  "Config/pak/sysreqs": "zlib1g-dev",
  "Repository": "https://bioc.r-universe.dev",
  "Date/Publication": "2026-05-22 06:10:02 UTC",
  "RemoteUrl": "https://github.com/bioc/pwalign",
  "RemoteRef": "HEAD",
  "RemoteSha": "f1991c73415ec8720cbdb57673fe57cd12715c23",
  "NeedsCompilation": "yes",
  "Packaged": {
    "Date": "2026-09-29 08:22:23 UTC",
    "User": "root"
  },
  "Author": "Patrick Aboyoun [aut],\nRobert Gentleman [aut],\nHervé Pagès [cre] (ORCID: <https://orcid.org/0009-0002-8272-4522>)",
  "Maintainer": "Hervé Pagès <hpages.on.github@gmail.com>",
  "_user": "bioc",
  "_type": "src",
  "_file": "pwalign_1.9.1.tar.gz",
  "_fileid": "https://r2.ropensci.org/d39c8aa7942066238b7d3868187d7906089e92ef78cdf1cc6c99fc11895d1045",
  "_filesize": 579907,
  "_sha256": "d39c8aa7942066238b7d3868187d7906089e92ef78cdf1cc6c99fc11895d1045",
  "_expires": "2027-01-07T08:29:38.000Z",
  "_created": "2026-09-29T08:22:23.000Z",
  "_published": "2026-09-29T08:29:43.637Z",
  "_bioccheck": {
    "error": 0,
    "warning": 3,
    "note": 6
  },
  "_host": "GitHub-Actions",
  "_buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633",
  "_status": "success",
  "_upstream": "https://github.com/bioc/pwalign",
  "_commit": {
    "id": "f1991c73415ec8720cbdb57673fe57cd12715c23",
    "author": "Hervé Pagès <hpages.on.github@gmail.com>",
    "committer": "Hervé Pagès <hpages.on.github@gmail.com>",
    "message": "pwalign 1.9.1: Import data() from BiocGenerics instead of utils\n",
    "time": 1779430202
  },
  "_maintainer": {
    "name": "Hervé Pagès",
    "email": "hpages.on.github@gmail.com",
    "login": "hpages",
    "linkedin": "in/hervé-pagès-5038527",
    "description": "",
    "uuid": 8810451,
    "orcid": "0009-0002-8272-4522"
  },
  "_distro": "resolute",
  "_jobs": [
    {
      "job": 109320493177,
      "time": 156,
      "config": "bioc-checks",
      "r": "4.6.1",
      "check": "WARNING",
      "artifact": "11020269214"
    },
    {
      "job": 109320493403,
      "time": 228,
      "config": "linux-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11020709718"
    },
    {
      "job": 109320493521,
      "time": 282,
      "config": "linux-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11021197540"
    },
    {
      "job": 109320493419,
      "time": 150,
      "config": "linux-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11020019608"
    },
    {
      "job": 109320493432,
      "time": 264,
      "config": "linux-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11021275538"
    },
    {
      "job": 109320493322,
      "time": 152,
      "config": "macos-oldrel-arm64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11021285191"
    },
    {
      "job": 109320493442,
      "time": 229,
      "config": "macos-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11021068675"
    },
    {
      "job": 109320493437,
      "time": 202,
      "config": "macos-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11020659849"
    },
    {
      "job": 109320493357,
      "time": 355,
      "config": "macos-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11021018992"
    },
    {
      "job": 109319283903,
      "time": 215,
      "config": "source",
      "r": "4.6.1",
      "check": "OK",
      "artifact": "11021127305"
    },
    {
      "job": 109320493087,
      "time": 105,
      "config": "wasm-release",
      "r": "4.6.0",
      "check": "OK",
      "artifact": "11021275020"
    },
    {
      "job": 109320493463,
      "time": 240,
      "config": "windows-devel-arm64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11021385162"
    },
    {
      "job": 109320493461,
      "time": 203,
      "config": "windows-devel-x86_64",
      "r": "4.7.0",
      "check": "NOTE",
      "artifact": "11020854412"
    },
    {
      "job": 109320493315,
      "time": 130,
      "config": "windows-oldrel-x86_64",
      "r": "4.5.3",
      "check": "NOTE",
      "artifact": "11020689331"
    },
    {
      "job": 109320493355,
      "time": 262,
      "config": "windows-release-arm64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11020284514"
    },
    {
      "job": 109320493316,
      "time": 128,
      "config": "windows-release-x86_64",
      "r": "4.6.1",
      "check": "NOTE",
      "artifact": "11021221112"
    }
  ],
  "_registered": true,
  "_dependencies": [
    {
      "package": "BiocGenerics",
      "version": ">= 0.59.3",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "Depends"
    },
    {
      "package": "IRanges",
      "role": "Depends"
    },
    {
      "package": "Biostrings",
      "version": ">= 2.71.5",
      "role": "Depends"
    },
    {
      "package": "S4Vectors",
      "role": "LinkingTo"
    },
    {
      "package": "IRanges",
      "role": "LinkingTo"
    },
    {
      "package": "XVector",
      "role": "LinkingTo"
    },
    {
      "package": "Biostrings",
      "role": "LinkingTo"
    },
    {
      "package": "methods",
      "role": "Imports"
    },
    {
      "package": "utils",
      "role": "Imports"
    },
    {
      "package": "RUnit",
      "role": "Suggests"
    },
    {
      "package": "Rmpi",
      "role": "Enhances"
    }
  ],
  "_owner": "bioc",
  "_selfowned": true,
  "_usedby": 113,
  "_updates": [
    {
      "week": "2025-44",
      "n": 3
    },
    {
      "week": "2026-18",
      "n": 3
    },
    {
      "week": "2026-21",
      "n": 1
    }
  ],
  "_tags": [],
  "_bioc": [
    {
      "branch": "devel",
      "version": "1.9.1",
      "bioc": "3.24"
    },
    {
      "branch": "release",
      "version": "1.8.0",
      "bioc": "3.23"
    }
  ],
  "_topics": [
    "alignment",
    "sequencematching",
    "sequencing",
    "genetics",
    "bioconductor-package"
  ],
  "_stars": 1,
  "_contributors": [
    {
      "user": "hpages",
      "count": 20,
      "uuid": 8810451
    },
    {
      "user": "jwokaty",
      "count": 11,
      "uuid": 1744257
    }
  ],
  "_userbio": {
    "uuid": 2286807,
    "type": "organization",
    "name": "Bioconductor",
    "followers": 470,
    "description": "Software for the analysis and comprehension of high-throughput genomic data"
  },
  "_downloads": {
    "count": 13495,
    "source": "https://www.bioconductor.org/packages/stats/bioc/pwalign"
  },
  "_devurl": "https://github.com/bioconductor/pwalign",
  "_searchresults": 1,
  "_rbuild": "4.6.1",
  "_assets": [
    "extra/citation.cff",
    "extra/citation.html",
    "extra/citation.json",
    "extra/citation.txt",
    "extra/contents.json",
    "extra/manual.pdf",
    "extra/NEWS.html",
    "extra/NEWS.txt",
    "extra/pwalign.html",
    "extra/readme.html",
    "extra/readme.md"
  ],
  "_homeurl": "https://github.com/bioconductor/pwalign",
  "_realowner": "bioc",
  "_cranurl": false,
  "_exports": [
    "aligned",
    "alignedPattern",
    "alignedSubject",
    "as.matrix",
    "compareStrings",
    "consensusMatrix",
    "coverage",
    "deletion",
    "end",
    "errorSubstitutionMatrices",
    "indel",
    "insertion",
    "mismatch",
    "mismatchSummary",
    "mismatchTable",
    "nchar",
    "nedit",
    "nindel",
    "nmatch",
    "nmismatch",
    "nucleotideSubstitutionMatrix",
    "pairwiseAlignment",
    "PairwiseAlignments",
    "PairwiseAlignmentsSingleSubject",
    "parallel_slot_names",
    "parallelVectorNames",
    "pattern",
    "pid",
    "qualitySubstitutionMatrices",
    "score",
    "show",
    "start",
    "stringDist",
    "subject",
    "summary",
    "toString",
    "type",
    "unaligned",
    "Views",
    "width",
    "writePairwiseAlignments"
  ],
  "_datasets": [
    {
      "name": "BLOSUM100",
      "title": "Predefined scoring matrices",
      "object": "BLOSUM100",
      "file": "BLOSUM100.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "Z",
        "X",
        "*"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "BLOSUM45",
      "title": "Predefined scoring matrices",
      "object": "BLOSUM45",
      "file": "BLOSUM45.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "J",
        "Z",
        "X",
        "*"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "BLOSUM50",
      "title": "Predefined scoring matrices",
      "object": "BLOSUM50",
      "file": "BLOSUM50.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "Z",
        "X",
        "*"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "BLOSUM62",
      "title": "Predefined scoring matrices",
      "object": "BLOSUM62",
      "file": "BLOSUM62.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "J",
        "Z",
        "X",
        "*"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "BLOSUM80",
      "title": "Predefined scoring matrices",
      "object": "BLOSUM80",
      "file": "BLOSUM80.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "J",
        "Z",
        "X",
        "*"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "PAM120",
      "title": "Predefined scoring matrices",
      "object": "PAM120",
      "file": "PAM120.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "Z",
        "X",
        "*"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "PAM250",
      "title": "Predefined scoring matrices",
      "object": "PAM250",
      "file": "PAM250.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "Z",
        "X",
        "*"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "PAM30",
      "title": "Predefined scoring matrices",
      "object": "PAM30",
      "file": "PAM30.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "J",
        "Z",
        "X",
        "*"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "PAM40",
      "title": "Predefined scoring matrices",
      "object": "PAM40",
      "file": "PAM40.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "Z",
        "X",
        "*"
      ],
      "rows": 24,
      "table": true,
      "tojson": true
    },
    {
      "name": "PAM70",
      "title": "Predefined scoring matrices",
      "object": "PAM70",
      "file": "PAM70.rda",
      "class": [
        "matrix",
        "array"
      ],
      "fields": [
        "A",
        "R",
        "N",
        "D",
        "C",
        "Q",
        "E",
        "G",
        "H",
        "I",
        "L",
        "K",
        "M",
        "F",
        "P",
        "S",
        "T",
        "W",
        "Y",
        "V",
        "B",
        "J",
        "Z",
        "X",
        "*"
      ],
      "rows": 25,
      "table": true,
      "tojson": true
    },
    {
      "name": "phiX174Phage",
      "title": "Versions of bacteriophage phiX174 complete genome and sample short reads",
      "object": "phiX174Phage",
      "file": "phiX174Phage.rda",
      "class": [
        "DNAStringSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "quPhiX174",
      "title": "Versions of bacteriophage phiX174 complete genome and sample short reads",
      "object": "srPhiX174",
      "file": "srPhiX174.rda",
      "class": [
        "BStringSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "srPhiX174",
      "title": "Versions of bacteriophage phiX174 complete genome and sample short reads",
      "object": "srPhiX174",
      "file": "srPhiX174.rda",
      "class": [
        "DNAStringSet"
      ],
      "fields": [],
      "table": false,
      "tojson": false
    },
    {
      "name": "wtPhiX174",
      "title": "Versions of bacteriophage phiX174 complete genome and sample short reads",
      "object": "srPhiX174",
      "file": "srPhiX174.rda",
      "class": [
        "integer"
      ],
      "fields": [],
      "table": false,
      "tojson": true
    }
  ],
  "_help": [
    {
      "page": "align-utils",
      "title": "Utility functions related to sequence alignment",
      "topics": [
        "align-utils",
        "compareStrings",
        "compareStrings,AlignedXStringSet0,AlignedXStringSet0-method",
        "compareStrings,character,character-method",
        "compareStrings,PairwiseAlignments,missing-method",
        "compareStrings,XString,XString-method",
        "compareStrings,XStringSet,XStringSet-method",
        "consensusMatrix,PairwiseAlignmentsSingleSubject-method",
        "coverage,AlignedXStringSet0-method",
        "coverage,PairwiseAlignmentsSingleSubject-method",
        "coverage,PairwiseAlignmentsSingleSubjectSummary-method",
        "mismatch,AlignedXStringSet0,missing-method",
        "mismatchSummary",
        "mismatchSummary,AlignedXStringSet0-method",
        "mismatchSummary,PairwiseAlignmentsSingleSubject-method",
        "mismatchSummary,PairwiseAlignmentsSingleSubjectSummary-method",
        "mismatchSummary,QualityAlignedXStringSet-method",
        "mismatchTable",
        "mismatchTable,AlignedXStringSet0-method",
        "mismatchTable,PairwiseAlignments-method",
        "mismatchTable,QualityAlignedXStringSet-method",
        "nedit",
        "nedit,PairwiseAlignments-method",
        "nedit,PairwiseAlignmentsSingleSubjectSummary-method",
        "nmatch,PairwiseAlignments,missing-method",
        "nmatch,PairwiseAlignmentsSingleSubjectSummary,missing-method",
        "nmismatch,AlignedXStringSet0,missing-method",
        "nmismatch,PairwiseAlignments,missing-method",
        "nmismatch,PairwiseAlignmentsSingleSubjectSummary,missing-method"
      ]
    },
    {
      "page": "AlignedXStringSet-class",
      "title": "AlignedXStringSet and QualityAlignedXStringSet objects",
      "topics": [
        "aligned",
        "aligned,AlignedXStringSet0-method",
        "AlignedXStringSet",
        "AlignedXStringSet-class",
        "AlignedXStringSet0",
        "AlignedXStringSet0-class",
        "as.character,AlignedXStringSet0-method",
        "class:AlignedXStringSet",
        "class:AlignedXStringSet0",
        "class:QualityAlignedXStringSet",
        "end,AlignedXStringSet0-method",
        "indel",
        "indel,AlignedXStringSet0-method",
        "nchar,AlignedXStringSet0-method",
        "nindel",
        "nindel,AlignedXStringSet0-method",
        "parallelVectorNames,AlignedXStringSet0-method",
        "parallel_slot_names,AlignedXStringSet0-method",
        "QualityAlignedXStringSet",
        "QualityAlignedXStringSet-class",
        "ranges,AlignedXStringSet0-method",
        "seqtype,AlignedXStringSet0-method",
        "show,AlignedXStringSet0-method",
        "start,AlignedXStringSet0-method",
        "toString,AlignedXStringSet0-method",
        "unaligned",
        "unaligned,AlignedXStringSet0-method",
        "width,AlignedXStringSet0-method"
      ]
    },
    {
      "page": "InDel-class",
      "title": "InDel objects",
      "topics": [
        "class:InDel",
        "deletion",
        "deletion,InDel-method",
        "InDel",
        "InDel-class",
        "insertion",
        "insertion,InDel-method"
      ]
    },
    {
      "page": "pairwiseAlignment",
      "title": "Optimal Pairwise Alignment",
      "topics": [
        "pairwiseAlignment",
        "pairwiseAlignment,ANY,ANY-method",
        "pairwiseAlignment,ANY,QualityScaledXStringSet-method",
        "pairwiseAlignment,QualityScaledXStringSet,ANY-method",
        "pairwiseAlignment,QualityScaledXStringSet,QualityScaledXStringSet-method"
      ]
    },
    {
      "page": "PairwiseAlignments-class",
      "title": "PairwiseAlignments, PairwiseAlignmentsSingleSubject, and PairwiseAlignmentsSingleSubjectSummary objects",
      "topics": [
        "aligned,PairwiseAlignmentsSingleSubject-method",
        "alignedPattern",
        "alignedPattern,PairwiseAlignments-method",
        "alignedSubject",
        "alignedSubject,PairwiseAlignments-method",
        "as.character,PairwiseAlignmentsSingleSubject-method",
        "as.matrix,PairwiseAlignmentsSingleSubject-method",
        "class:PairwiseAlignments",
        "class:PairwiseAlignmentsSingleSubject",
        "class:PairwiseAlignmentsSingleSubjectSummary",
        "deletion,PairwiseAlignments-method",
        "indel,PairwiseAlignments-method",
        "insertion,PairwiseAlignments-method",
        "length,PairwiseAlignmentsSingleSubjectSummary-method",
        "nchar,PairwiseAlignments-method",
        "nchar,PairwiseAlignmentsSingleSubjectSummary-method",
        "nindel,PairwiseAlignments-method",
        "nindel,PairwiseAlignmentsSingleSubjectSummary-method",
        "PairwiseAlignments",
        "PairwiseAlignments,character,character-method",
        "PairwiseAlignments,character,missing-method",
        "PairwiseAlignments,XString,XString-method",
        "PairwiseAlignments,XStringSet,missing-method",
        "PairwiseAlignments-class",
        "PairwiseAlignmentsSingleSubject",
        "PairwiseAlignmentsSingleSubject,character,character-method",
        "PairwiseAlignmentsSingleSubject,character,missing-method",
        "PairwiseAlignmentsSingleSubject,XString,XString-method",
        "PairwiseAlignmentsSingleSubject,XStringSet,missing-method",
        "PairwiseAlignmentsSingleSubject-class",
        "PairwiseAlignmentsSingleSubjectSummary",
        "PairwiseAlignmentsSingleSubjectSummary-class",
        "parallel_slot_names,PairwiseAlignments-method",
        "pattern",
        "pattern,PairwiseAlignments-method",
        "score,PairwiseAlignments-method",
        "score,PairwiseAlignmentsSingleSubjectSummary-method",
        "seqtype,PairwiseAlignments-method",
        "show,PairwiseAlignments-method",
        "show,PairwiseAlignmentsSingleSubjectSummary-method",
        "subject,PairwiseAlignments-method",
        "summary,PairwiseAlignmentsSingleSubject-method",
        "toString,PairwiseAlignmentsSingleSubject-method",
        "type",
        "type,PairwiseAlignments-method",
        "type,PairwiseAlignmentsSingleSubjectSummary-method",
        "Views,PairwiseAlignmentsSingleSubject-method"
      ]
    },
    {
      "page": "PairwiseAlignments-io",
      "title": "Write a PairwiseAlignments object to a file",
      "topics": [
        "PairwiseAlignments-io",
        "writePairwiseAlignments"
      ]
    },
    {
      "page": "phiX174Phage",
      "title": "Versions of bacteriophage phiX174 complete genome and sample short reads",
      "topics": [
        "phiX174Phage",
        "quPhiX174",
        "srPhiX174",
        "wtPhiX174"
      ]
    },
    {
      "page": "pid",
      "title": "Percent Sequence Identity",
      "topics": [
        "pid",
        "pid,PairwiseAlignments-method"
      ]
    },
    {
      "page": "predefined_scoring_matrices",
      "title": "Predefined scoring matrices",
      "topics": [
        "BLOSUM100",
        "BLOSUM45",
        "BLOSUM50",
        "BLOSUM62",
        "BLOSUM80",
        "PAM120",
        "PAM250",
        "PAM30",
        "PAM40",
        "PAM70",
        "predefined_scoring_matrices"
      ]
    },
    {
      "page": "stringDist",
      "title": "String Distance/Alignment Score Matrix",
      "topics": [
        "stringDist",
        "stringDist,character-method",
        "stringDist,QualityScaledXStringSet-method",
        "stringDist,XStringSet-method"
      ]
    },
    {
      "page": "substitution_matrices",
      "title": "Utilities to generate substitution matrices",
      "topics": [
        "errorSubstitutionMatrices",
        "nucleotideSubstitutionMatrix",
        "qualitySubstitutionMatrices",
        "substitution_matrices"
      ]
    }
  ],
  "_readme": "https://github.com/bioc/pwalign/raw/HEAD/README.md",
  "_rundeps": [
    "BiocGenerics",
    "Biostrings",
    "crayon",
    "generics",
    "IRanges",
    "S4Vectors",
    "Seqinfo",
    "XVector"
  ],
  "_vignettes": [
    {
      "source": "PairwiseAlignments.Rnw",
      "filename": "PairwiseAlignments.pdf",
      "title": "Pairwise Sequence Alignments",
      "engine": "utils::Sweave",
      "headings": [
        "Introduction",
        "Pairwise Sequence Alignment Problems",
        "Main Pairwise Sequence Alignment Function",
        "Pairwise Sequence Alignment Classes",
        "Pairwise Sequence Alignment Helper Functions",
        "Edit Distances",
        "Application: Using Evolutionary Models in Protein Alignments",
        "Application: Removing Adapters from Sequence Reads",
        "Application: Quality Assurance in Sequencing Experiments",
        "Computation Profiling",
        "Computing alignment consensus matrices",
        "Exercise Answers",
        "Session Information"
      ],
      "created": "2024-03-21 02:43:00",
      "modified": "2024-03-21 17:36:59",
      "commits": 3
    }
  ],
  "_score": 7.836463846151299,
  "_indexed": true,
  "_nocasepkg": "pwalign",
  "_universes": [
    "bioc",
    "hpages",
    "bioconductor"
  ],
  "_binaries": [
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.1",
      "date": "2026-09-29T08:25:18.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/d332d83097bbaed2530c479fd6f172a3fa2f5c1e9d3c6f29e09a6b065d0f7ab2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.7.0",
      "os": "linux",
      "version": "1.9.1",
      "date": "2026-09-29T08:26:06.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/56baa0a2d4fe42ede0ffda49779d2347ad635d250ca4e82f22df2873a95a438f",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.1",
      "date": "2026-09-29T08:24:23.000Z",
      "distro": "resolute",
      "arch": "aarch64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/282ac504043744a9256021b427fb3d2289de6a7f9c52ad164eeda273923c9792",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.1",
      "os": "linux",
      "version": "1.9.1",
      "date": "2026-09-29T08:25:59.000Z",
      "distro": "resolute",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/de9bc794b29d88ed566518abea6ed639decd62ab661a20a4ae55eb38f6e68f21",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.1",
      "date": "2026-09-29T08:24:54.000Z",
      "arch": "aarch64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/4689f62daf8ab61d511b845f9373b2abdf5b0c3ddf902acfc3abc7824fdff328",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.5.3",
      "os": "mac",
      "version": "1.9.1",
      "date": "2026-09-29T08:25:38.000Z",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/cc0563da058724908f606e5690c94b9735b622fb6ebb6e370f09f7b696fb10a4",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.1",
      "date": "2026-09-29T08:25:19.000Z",
      "arch": "aarch64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/61b36a9a538bd66d5dd7e100889f0a38c8c6a1a81bc076c9bf8f892c19460512",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.1",
      "os": "mac",
      "version": "1.9.1",
      "date": "2026-09-29T08:26:47.000Z",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/5ce47f256552cf9f19f7410635ac7cdd093f492457df146e289598ce3be2bcc2",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.0",
      "os": "wasm",
      "version": "1.9.1",
      "date": "2026-09-29T08:24:27.000Z",
      "arch": "emscripten",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/947e3c68063200f159304143432782693088f7a50822099203cf087e5f5b6586",
      "status": "success",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.1",
      "date": "2026-09-29T08:25:25.000Z",
      "arch": "aarch64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/4a52408b70c4562efdc1864832e3c97e97b4449bd814a90560d96aad55a54439",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.7.0",
      "os": "win",
      "version": "1.9.1",
      "date": "2026-09-29T08:23:47.000Z",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/cb7ebf85265c21e582c97104fcd6a3c69c970223275c936526d5ee78ab511240",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.5.3",
      "os": "win",
      "version": "1.9.1",
      "date": "2026-09-29T08:23:27.000Z",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/edb16b89364ccc8267af7b093fc2dd0e565b34d45ef18a591a7e47707d770740",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.1",
      "date": "2026-09-29T08:25:52.000Z",
      "arch": "aarch64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/133577d00f678e1f86b6e6ddd9dfb23099c1bc4ab9cf45b22254dd89da4751b3",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    },
    {
      "r": "4.6.1",
      "os": "win",
      "version": "1.9.1",
      "date": "2026-09-29T08:23:25.000Z",
      "arch": "x86_64",
      "commit": "f1991c73415ec8720cbdb57673fe57cd12715c23",
      "fileid": "https://r2.ropensci.org/def47cf1a015c71712db40899192cac23d07ed701adb1b3869eb0bc56ea04c9c",
      "status": "success",
      "check": "NOTE",
      "buildurl": "https://github.com/r-universe/bioc/actions/runs/36541921633"
    }
  ]
}