{ "_id": "6a1ac16a1d7bb097a09d860a", "Package": "muscle", "Type": "Package", "Title": "Multiple Sequence Alignment with MUSCLE", "Version": "3.55.0", "Date": "2012-10-05", "Author": "Algorithm by Robert C. Edgar. R port by Alex T. Kalinka.", "Maintainer": "Alex T. Kalinka ", "Description": "MUSCLE performs multiple sequence alignments of nucleotide\nor amino acid sequences.", "biocViews": "MultipleSequenceAlignment, Alignment, Sequencing, Genetics,\nSequenceMatching, DataImport", "License": "Unlimited", "URL": "http://www.drive5.com/muscle/", "LazyLoad": "yes", "LazyData": "yes", "NeedsCompilation": "yes", "Config/pak/sysreqs": "zlib1g-dev", "Repository": "https://bioc.r-universe.dev", "Date/Publication": "2026-04-28 12:40:42 UTC", "RemoteUrl": "https://github.com/bioc/muscle", "RemoteRef": "HEAD", "RemoteSha": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "Packaged": { "Date": "2026-05-30 07:27:45 UTC", "User": "root" }, "MD5sum": "c6b06fc043ef41639581b521a1fc193b", "_user": "bioc", "_type": "src", "_file": "muscle_3.55.0.tar.gz", "_fileid": "3048de2e5850f9d71f2651ba220a639220fca9f6302d4c15ac4b2c76f2a45136", "_filesize": 391048, "_sha256": "3048de2e5850f9d71f2651ba220a639220fca9f6302d4c15ac4b2c76f2a45136", "_created": "2026-05-30T07:27:45.000Z", "_published": "2026-05-30T10:52:26.625Z", "_jobs": [ { "job": 78633516323, "time": 168, "config": "bioc-checks", "r": "4.6.0", "check": "ERROR", "artifact": "7306487730" }, { "job": 78633516338, "time": 168, "config": "linux-devel-arm64", "r": "4.7.0", "check": "WARNING", "artifact": "7306487693" }, { "job": 78633516339, "time": 236, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "WARNING", "artifact": "7306494883" }, { "job": 78633516327, "time": 174, "config": "linux-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7306488324" }, { "job": 78633516328, "time": 192, "config": "linux-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306490314" }, { "job": 78633516337, "time": 161, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "WARNING", "artifact": "7307605410" }, { "job": 78633516346, "time": 336, "config": "macos-oldrel-x86_64", "r": "4.5.3", "check": "WARNING", "artifact": "7306577360" }, { "job": 78633516340, "time": 118, "config": "macos-release-arm64", "r": "4.6.0", "check": "WARNING", "artifact": "7307601887" }, { "job": 78633516336, "time": 358, "config": "macos-release-x86_64", "r": "4.6.0", "check": "WARNING", "artifact": "7306581268" }, { "job": 78633309158, "time": 222, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7306468616" }, { "job": 78633516324, "time": 144, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7306485103" }, { "job": 78633516330, "time": 203, "config": "windows-devel", "r": "4.7.0", "check": "WARNING", "artifact": "7306491396" }, { "job": 78633516347, "time": 201, "config": "windows-oldrel", "r": "4.5.3", "check": "WARNING", "artifact": "7306491201" }, { "job": 78633516325, "time": 213, "config": "windows-release", "r": "4.6.0", "check": "WARNING", "artifact": "7306492535" } ], "_bioccheck": { "error": 1, "warning": 1, "note": 12 }, "_buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://github.com/bioc/muscle", "_commit": { "id": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "author": "A Wokaty ", "committer": "A Wokaty ", "message": "bump x.y.z version to odd y following creation of RELEASE_3_23 branch\n", "time": 1777380042 }, "_maintainer": { "name": "Alex T. Kalinka", "email": "alex.t.kalinka@gmail.com", "login": "alextkalinka", "description": "", "uuid": 61851571 }, "_distro": "noble", "_registered": true, "_dependencies": [ { "package": "Biostrings", "role": "Depends" } ], "_owner": "bioc", "_selfowned": true, "_usedby": 0, "_updates": [ { "week": "2025-44", "n": 2 }, { "week": "2026-18", "n": 2 } ], "_tags": [], "_bioc": [ { "branch": "devel", "version": "3.55.0", "bioc": "3.24" }, { "branch": "release", "version": "3.54.0", "bioc": "3.23" } ], "_topics": [ "multiplesequencealignment", "alignment", "sequencing", "genetics", "sequencematching", "dataimport", "cpp" ], "_userbio": { "uuid": 2286807, "type": "organization", "name": "Bioconductor", "description": "Software for the analysis and comprehension of high-throughput genomic data" }, "_downloads": { "count": 756, "source": "https://www.bioconductor.org/packages/stats/bioc/muscle" }, "_mentions": 166, "_searchresults": 102, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/muscle.html", "extra/NEWS.html", "extra/NEWS.txt", "manual.pdf" ], "_realowner": "bioc", "_cranurl": false, "_releases": [ { "version": "3.8.31-0", "date": "2012-10-15" }, { "version": "3.8.31-1", "date": "2013-03-29" }, { "version": "3.8.31-2", "date": "2014-05-07" }, { "version": "3.8.31-3", "date": "2014-07-04" }, { "version": "3.8.31-4", "date": "2014-07-07" } ], "_exports": [ ".muscleR", "muscle" ], "_datasets": [ { "name": "umax", "title": "Unaligned MAX sequences", "object": "umax", "class": [ "DNAStringSet" ], "fields": [], "table": false, "tojson": false } ], "_help": [ { "page": "muscle-package", "title": "Multiple Sequence Alignment", "topics": [ "muscle-package" ] }, { "page": "muscle", "title": "Multiple Sequence Alignment", "topics": [ "muscle" ] }, { "page": "umax", "title": "Unaligned MAX sequences", "topics": [ "umax" ] } ], "_rundeps": [ "BiocGenerics", "Biostrings", "crayon", "generics", "IRanges", "S4Vectors", "Seqinfo", "XVector" ], "_sysdeps": [ { "shlib": "libstdc++", "package": "libstdc++6", "source": "gcc", "version": "14.2.0-4ubuntu2~24.04.1", "name": "c++", "homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "muscle-vignette.Rnw", "filename": "muscle-vignette.pdf", "title": "A guide to using muscle", "engine": "utils::Sweave", "headings": [], "created": "2015-03-07 00:46:17", "modified": "2015-03-07 00:46:17", "commits": 1 } ], "_score": 5.309630167425899, "_indexed": true, "_nocasepkg": "muscle", "_universes": [ "bioc", "alextkalinka" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "3.55.0", "date": "2026-05-30T07:30:14.000Z", "distro": "noble", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "1ae4a9f72f989b6177b159057ed0b17c3edc222b95853c620a1e3e0c2989623e", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.7.0", "os": "linux", "version": "3.55.0", "date": "2026-05-30T07:31:04.000Z", "distro": "noble", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "fac66f971420cff8d8ba4463df5d1cf74abbc6db44f8de951992282e3bfe5d15", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.6.0", "os": "linux", "version": "3.55.0", "date": "2026-05-30T07:30:17.000Z", "distro": "noble", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "c01278d471499aef2958c65fbef7dbb1cbfe6e8054249eac17dfc12f18d33014", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.6.0", "os": "linux", "version": "3.55.0", "date": "2026-05-30T07:30:32.000Z", "distro": "noble", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "48d6704bb5a633fbe1298b8679fc067ec7f01a0383fe062131a929835a087730", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.5.3", "os": "mac", "version": "3.55.0", "date": "2026-05-30T10:43:12.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "16f3c776d727091952cad8344530e798e584100c3bf1c8319913e7edbeb6f0b0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.5.3", "os": "mac", "version": "3.55.0", "date": "2026-05-30T07:43:10.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "75107f30a9dd5dc8f7ee386ee7a0e10ab2260765de880ca6979705b327313179", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.6.0", "os": "mac", "version": "3.55.0", "date": "2026-05-30T10:42:55.000Z", "arch": "aarch64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "f6d5ccbfd9eceeab5c0fe2aef2d89c0cb4b431fa0b845414ec7c7cbe2179d216", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.6.0", "os": "mac", "version": "3.55.0", "date": "2026-05-30T07:43:48.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "f810ddbcbf8debf6f17dd49d8943fc5de3c7e22bc07c0ca299c1d2a0cb0ff9b0", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.6.0", "os": "wasm", "version": "3.55.0", "date": "2026-05-30T07:30:12.000Z", "arch": "emscripten", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "5feafff205b71ef7fad035d100c162b93cc0b26f345c54c490b522d7f8a75e22", "status": "success", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.7.0", "os": "win", "version": "3.55.0", "date": "2026-05-30T07:29:26.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "272349ed75053af8300136fbce27f296bd401d78ae1e14e4d753884a707686bc", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.5.3", "os": "win", "version": "3.55.0", "date": "2026-05-30T07:29:19.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "42ba533e074651aad5a3fed7a3aea7aad0b71fa0bf3fa68615c9e83ea375972b", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" }, { "r": "4.6.0", "os": "win", "version": "3.55.0", "date": "2026-05-30T07:29:27.000Z", "arch": "x86_64", "commit": "2446ca4ab6e585b3aca01b365cfff217f3953ec8", "fileid": "47da5a3ce861d627fbd6a6031002876e065d50081288373e6a1b21070d32dad5", "status": "success", "check": "WARNING", "buildurl": "https://github.com/r-universe/bioc/actions/runs/26677998962" } ] }