{"id":39448,"name":"multiplesequencealign","description":"A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.","url":"https://github.com/nf-core/multiplesequencealign","last_synced_at":"2025-09-05T08:11:42.043Z","repository":{"id":183664724,"uuid":"670209670","full_name":"nf-core/multiplesequencealign","owner":"nf-core","description":"A pipeline to run and systematically evaluate Multiple Sequence Alignment (MSA) methods.","archived":false,"fork":false,"pushed_at":"2025-07-09T08:24:51.000Z","size":20538,"stargazers_count":35,"open_issues_count":12,"forks_count":14,"subscribers_count":163,"default_branch":"master","last_synced_at":"2025-07-09T09:35:20.470Z","etag":null,"topics":["nextflow","nf-core","pipeline","workflow"],"latest_commit_sha":null,"homepage":"https://nf-co.re/multiplesequencealign","language":"Nextflow","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/nf-core.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":"CITATIONS.md","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2023-07-24T14:30:12.000Z","updated_at":"2025-05-27T19:24:34.000Z","dependencies_parsed_at":"2025-05-22T16:37:24.736Z","dependency_job_id":null,"html_url":"https://github.com/nf-core/multiplesequencealign","commit_stats":null,"previous_names":["luisas/nf-core-msa","joseespinosa/nf-core-msa"],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/nf-core/multiplesequencealign","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","download_url":"https://codeload.github.com/nf-core/multiplesequencealign/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":273728154,"owners_count":25157136,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","status":"online","status_checked_at":"2025-09-05T02:00:09.113Z","response_time":402,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"owner":{"login":"nf-core","name":"nf-core","uuid":"35520196","kind":"organization","description":"A community effort to collect a curated set of analysis pipelines built using Nextflow.","email":"core@nf-co.re","website":"http://nf-co.re","location":null,"twitter":"nf_core","company":null,"icon_url":"https://avatars.githubusercontent.com/u/35520196?v=4","repositories_count":84,"last_synced_at":"2023-03-01T20:50:19.252Z","metadata":{"has_sponsors_listing":false},"html_url":"https://github.com/nf-core","funding_links":[],"total_stars":null,"followers":null,"following":null,"created_at":"2022-11-12T16:29:01.932Z","updated_at":"2023-03-01T20:50:19.281Z","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nf-core/repositories"},"packages":[],"commits":{"message":"Repository syncing started."},"issues_stats":{"full_name":"nf-core/multiplesequencealign","html_url":"https://github.com/nf-core/multiplesequencealign","last_synced_at":"2025-08-31T13:28:31.312Z","status":null,"issues_count":19,"pull_requests_count":34,"avg_time_to_close_issue":2008753.4,"avg_time_to_close_pull_request":282791.3076923077,"issues_closed_count":10,"pull_requests_closed_count":26,"pull_request_authors_count":4,"issue_authors_count":5,"avg_comments_per_issue":0.5263157894736842,"avg_comments_per_pull_request":0.7941176470588235,"merged_pull_requests_count":24,"bot_issues_count":0,"bot_pull_requests_count":0,"past_year_issues_count":19,"past_year_pull_requests_count":34,"past_year_avg_time_to_close_issue":2008753.4,"past_year_avg_time_to_close_pull_request":282791.3076923077,"past_year_issues_closed_count":10,"past_year_pull_requests_closed_count":26,"past_year_pull_request_authors_count":4,"past_year_issue_authors_count":5,"past_year_avg_comments_per_issue":0.5263157894736842,"past_year_avg_comments_per_pull_request":0.7941176470588235,"past_year_bot_issues_count":0,"past_year_bot_pull_requests_count":0,"past_year_merged_pull_requests_count":24,"created_at":"2025-08-29T14:17:53.990Z","updated_at":"2025-09-03T04:44:25.993Z","repository_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign","issues_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories/nf-core%2Fmultiplesequencealign/issues","issue_labels_count":{"enhancement":40,"hackathon":10,"bug":9,"not urgent":3,"documentation":1,"duplicate":1},"pull_request_labels_count":{"enhancement":2},"issue_author_associations_count":{"COLLABORATOR":45,"NONE":3,"CONTRIBUTOR":3,"MEMBER":2},"pull_request_author_associations_count":{"COLLABORATOR":51,"MEMBER":22,"CONTRIBUTOR":11,"NONE":4},"issue_authors":{"luisas":45,"lrauschning":3,"JoseEspinosa":2,"jen-reeve":1,"random-annoym":1,"bxskdh":1},"pull_request_authors":{"luisas":51,"nf-core-bot":13,"lrauschning":9,"JoseEspinosa":7,"itrujnara":3,"mirpedrol":1,"alessiovignoli":1,"nvnieuwk":1,"maxulysse":1,"Joon-Klaps":1},"host":{"name":"GitHub","url":"https://github.com","kind":"github","last_synced_at":"2025-09-04T00:00:25.939Z","repositories_count":10081047,"issues_count":31277651,"pull_requests_count":96104459,"authors_count":10693669,"icon_url":"https://github.com/github.png","host_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/repositories","owners_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/owners","authors_url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors"},"past_year_issue_labels_count":{"enhancement":19,"bug":4,"documentation":1},"past_year_pull_request_labels_count":{},"past_year_issue_author_associations_count":{"COLLABORATOR":22,"NONE":3,"CONTRIBUTOR":1},"past_year_pull_request_author_associations_count":{"COLLABORATOR":39,"MEMBER":13,"NONE":1,"CONTRIBUTOR":1},"past_year_issue_authors":{"luisas":22,"bxskdh":1,"jen-reeve":1,"lrauschning":1,"random-annoym":1},"past_year_pull_request_authors":{"luisas":39,"nf-core-bot":8,"JoseEspinosa":3,"mirpedrol":1,"nvnieuwk":1,"maxulysse":1,"lrauschning":1},"maintainers":[{"login":"luisas","count":96,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/luisas"},{"login":"nf-core-bot","count":13,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"JoseEspinosa","count":9,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/JoseEspinosa"},{"login":"mirpedrol","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mirpedrol"},{"login":"maxulysse","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/maxulysse"}],"active_maintainers":[{"login":"luisas","count":61,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/luisas"},{"login":"nf-core-bot","count":8,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/nf-core-bot"},{"login":"JoseEspinosa","count":3,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/JoseEspinosa"},{"login":"mirpedrol","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/mirpedrol"},{"login":"maxulysse","count":1,"url":"https://issues.ecosyste.ms/api/v1/hosts/GitHub/authors/maxulysse"}]},"events":{"total":{"CreateEvent":8,"ReleaseEvent":2,"IssuesEvent":35,"WatchEvent":17,"DeleteEvent":1,"IssueCommentEvent":60,"PushEvent":70,"PullRequestEvent":69,"PullRequestReviewEvent":90,"PullRequestReviewCommentEvent":115,"ForkEvent":3},"last_year":{"CreateEvent":8,"ReleaseEvent":2,"IssuesEvent":35,"WatchEvent":17,"DeleteEvent":1,"IssueCommentEvent":60,"PushEvent":70,"PullRequestEvent":69,"PullRequestReviewEvent":90,"PullRequestReviewCommentEvent":115,"ForkEvent":3}},"keywords":["nextflow","nf-core","pipeline","workflow"],"dependencies":[{"ecosystem":"actions","filepath":".github/workflows/awsfulltest.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:28.781Z","updated_at":"2023-07-25T11:05:28.781Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/awsfulltest.yml","dependencies":[{"id":11996218577,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":11996218633,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/awstest.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:29.362Z","updated_at":"2023-07-25T11:05:29.362Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/awstest.yml","dependencies":[{"id":11996219333,"package_name":"seqeralabs/action-tower-launch","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":11996219334,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/branch.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:29.661Z","updated_at":"2023-07-25T11:05:29.661Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/branch.yml","dependencies":[{"id":11996219827,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/ci.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:29.853Z","updated_at":"2023-07-25T11:05:29.853Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/ci.yml","dependencies":[{"id":11996219890,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":11996219891,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/clean-up.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:30.183Z","updated_at":"2023-07-25T11:05:30.183Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/clean-up.yml","dependencies":[{"id":11996219944,"package_name":"actions/stale","ecosystem":"actions","requirements":"v7","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/fix-linting.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:30.369Z","updated_at":"2023-07-25T11:05:30.369Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/fix-linting.yml","dependencies":[{"id":11996220138,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":11996220139,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:30.477Z","updated_at":"2023-07-25T11:05:30.477Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/linting.yml","dependencies":[{"id":11996220205,"package_name":"actions/checkout","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":11996220206,"package_name":"actions/setup-node","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false},{"id":11996220207,"package_name":"psf/black","ecosystem":"actions","requirements":"stable","direct":true,"kind":"composite","optional":false},{"id":11996220208,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":11996220209,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":11996220210,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v4","direct":true,"kind":"composite","optional":false},{"id":11996220211,"package_name":"actions/upload-artifact","ecosystem":"actions","requirements":"v3","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/linting_comment.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:30.652Z","updated_at":"2023-07-25T11:05:30.652Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/linting_comment.yml","dependencies":[{"id":11996220372,"package_name":"dawidd6/action-download-artifact","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":11996220373,"package_name":"marocchino/sticky-pull-request-comment","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/multiqc/meta.yml","sha":null,"kind":"manifest","created_at":"2023-07-25T11:05:31.262Z","updated_at":"2023-07-25T11:05:31.262Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/multiqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/learnmsa/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-20T15:31:05.927Z","updated_at":"2023-10-20T15:31:05.927Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/learnmsa/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/muscle5/super5/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-20T15:31:06.162Z","updated_at":"2023-10-20T15:31:06.162Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/muscle5/super5/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-10-20T15:31:06.476Z","updated_at":"2023-10-20T15:31:06.476Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/clustalo/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-29T07:50:43.819Z","updated_at":"2023-09-29T07:50:43.819Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/clustalo/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/clustalo/guidetree/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-29T07:50:43.894Z","updated_at":"2023-09-29T07:50:43.894Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/clustalo/guidetree/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/famsa/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-29T07:50:43.963Z","updated_at":"2023-09-29T07:50:43.963Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/famsa/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/famsa/guidetree/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-29T07:50:44.124Z","updated_at":"2023-09-29T07:50:44.124Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/famsa/guidetree/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/kalign/align/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-29T07:50:44.234Z","updated_at":"2023-09-29T07:50:44.234Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/kalign/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/untar/meta.yml","sha":null,"kind":"manifest","created_at":"2023-09-29T07:50:44.401Z","updated_at":"2023-09-29T07:50:44.401Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/untar/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/csvtk/concat/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-15T13:41:47.806Z","updated_at":"2023-12-15T13:41:47.806Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/csvtk/concat/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/csvtk/join/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-15T13:41:47.965Z","updated_at":"2023-12-15T13:41:47.965Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/csvtk/join/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/alncompare/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-15T13:41:48.111Z","updated_at":"2023-12-15T13:41:48.111Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/alncompare/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/irmsd/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-15T13:41:48.126Z","updated_at":"2023-12-15T13:41:48.126Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/irmsd/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/seqreformat/meta.yml","sha":null,"kind":"manifest","created_at":"2023-12-15T13:41:48.185Z","updated_at":"2023-12-15T13:41:48.185Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/seqreformat/meta.yml","dependencies":[]},{"ecosystem":"actions","filepath":".github/workflows/download_pipeline.yml","sha":null,"kind":"manifest","created_at":"2024-02-07T10:43:50.808Z","updated_at":"2024-02-07T10:43:50.808Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/download_pipeline.yml","dependencies":[{"id":16089217246,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v1","direct":true,"kind":"composite","optional":false},{"id":16089217247,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v5","direct":true,"kind":"composite","optional":false},{"id":16089217248,"package_name":"eWaterCycle/setup-singularity","ecosystem":"actions","requirements":"v7","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/release-announcements.yml","sha":null,"kind":"manifest","created_at":"2024-02-07T10:43:51.157Z","updated_at":"2024-02-07T10:43:51.157Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/release-announcements.yml","dependencies":[{"id":16089217439,"package_name":"rzr/fediverse-action","ecosystem":"actions","requirements":"master","direct":true,"kind":"composite","optional":false},{"id":16089217440,"package_name":"actions/setup-python","ecosystem":"actions","requirements":"v5","direct":true,"kind":"composite","optional":false},{"id":16089217441,"package_name":"zentered/bluesky-post-action","ecosystem":"actions","requirements":"v0.1.0","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-28T12:42:59.891Z","updated_at":"2024-02-28T12:42:59.891Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/subworkflows/nf-core/utils_nextflow_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","sha":null,"kind":"manifest","created_at":"2024-02-28T12:42:59.895Z","updated_at":"2024-02-28T12:42:59.895Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/subworkflows/nf-core/utils_nfcore_pipeline/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/tcs/meta.yml","sha":null,"kind":"manifest","created_at":"2024-03-26T08:37:46.811Z","updated_at":"2024-03-26T08:37:46.811Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/tcs/meta.yml","dependencies":[]},{"ecosystem":"conda","filepath":"modules/nf-core/fastavalidator/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:13.316Z","updated_at":"2025-05-22T16:37:13.316Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/fastavalidator/environment.yml","dependencies":[{"id":23254676071,"package_name":"py_fasta_validator","ecosystem":"conda","requirements":"0.6.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/foldmason/createdb/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:13.494Z","updated_at":"2025-05-22T16:37:13.494Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/foldmason/createdb/environment.yml","dependencies":[{"id":23254676072,"package_name":"foldmason","ecosystem":"conda","requirements":"2.7bd21ed.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/foldmason/easymsa/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:14.499Z","updated_at":"2025-05-22T16:37:14.499Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/foldmason/easymsa/environment.yml","dependencies":[{"id":23254676073,"package_name":"foldmason","ecosystem":"conda","requirements":"2.7bd21ed.*","direct":true,"kind":"runtime","optional":false},{"id":23254676074,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/foldmason/msa2lddtreport/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:15.748Z","updated_at":"2025-05-22T16:37:15.748Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/foldmason/msa2lddtreport/environment.yml","dependencies":[{"id":23254676075,"package_name":"foldmason","ecosystem":"conda","requirements":"2.7bd21ed.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/mafft/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:16.021Z","updated_at":"2025-05-22T16:37:16.021Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/mafft/align/environment.yml","dependencies":[{"id":23254676076,"package_name":"mafft","ecosystem":"conda","requirements":"7.520.*","direct":true,"kind":"runtime","optional":false},{"id":23254676077,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/mafft/guidetree/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:17.295Z","updated_at":"2025-05-22T16:37:17.295Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/mafft/guidetree/environment.yml","dependencies":[{"id":23254676078,"package_name":"mafft","ecosystem":"conda","requirements":"7.525.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/magus/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:17.352Z","updated_at":"2025-05-22T16:37:17.352Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/magus/align/environment.yml","dependencies":[{"id":23254676079,"package_name":"magus-msa","ecosystem":"conda","requirements":"0.2.0.*","direct":true,"kind":"runtime","optional":false},{"id":23254676080,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/mtmalign/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:18.915Z","updated_at":"2025-05-22T16:37:18.915Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/mtmalign/align/environment.yml","dependencies":[{"id":23254676081,"package_name":"mtm-align","ecosystem":"conda","requirements":"20220104.*","direct":true,"kind":"runtime","optional":false},{"id":23254676135,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/pigz/compress/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:19.764Z","updated_at":"2025-05-22T16:37:19.764Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/pigz/compress/environment.yml","dependencies":[{"id":23254676140,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tcoffee/alncompare/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:19.831Z","updated_at":"2025-05-22T16:37:19.831Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/alncompare/environment.yml","dependencies":[{"id":23254676187,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false},{"id":23254676188,"package_name":"t-coffee","ecosystem":"conda","requirements":"13.46.0.919e8c6b.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tcoffee/consensus/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:20.589Z","updated_at":"2025-05-22T16:37:20.589Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/consensus/environment.yml","dependencies":[{"id":23254676307,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false},{"id":23254676308,"package_name":"t-coffee","ecosystem":"conda","requirements":"13.46.0.919e8c6b.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tcoffee/extractfrompdb/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:20.646Z","updated_at":"2025-05-22T16:37:20.646Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/extractfrompdb/environment.yml","dependencies":[{"id":23254676319,"package_name":"t-coffee","ecosystem":"conda","requirements":"13.46.0.919e8c6b.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tcoffee/irmsd/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:20.702Z","updated_at":"2025-05-22T16:37:20.702Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/irmsd/environment.yml","dependencies":[{"id":23254676322,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false},{"id":23254676323,"package_name":"t-coffee","ecosystem":"conda","requirements":"13.46.0.919e8c6b.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tcoffee/regressive/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:20.759Z","updated_at":"2025-05-22T16:37:20.759Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/regressive/environment.yml","dependencies":[{"id":23254676332,"package_name":"pigz","ecosystem":"conda","requirements":"2.8.*","direct":true,"kind":"runtime","optional":false},{"id":23254676333,"package_name":"t-coffee","ecosystem":"conda","requirements":"13.46.0.919e8c6b.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"conda","filepath":"modules/nf-core/tcoffee/seqreformat/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:20.815Z","updated_at":"2025-05-22T16:37:20.815Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/seqreformat/environment.yml","dependencies":[{"id":23254676349,"package_name":"t-coffee","ecosystem":"conda","requirements":"13.46.0.919e8c6b.*","direct":true,"kind":"runtime","optional":false}]},{"ecosystem":"pypi","filepath":"modules/nf-core/clustalo/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.354Z","updated_at":"2025-05-22T16:37:21.354Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/clustalo/align/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/clustalo/guidetree/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.399Z","updated_at":"2025-05-22T16:37:21.399Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/clustalo/guidetree/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/csvtk/concat/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.444Z","updated_at":"2025-05-22T16:37:21.444Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/csvtk/concat/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/csvtk/join/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.489Z","updated_at":"2025-05-22T16:37:21.489Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/csvtk/join/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/famsa/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.534Z","updated_at":"2025-05-22T16:37:21.534Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/famsa/align/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/famsa/guidetree/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.579Z","updated_at":"2025-05-22T16:37:21.579Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/famsa/guidetree/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/kalign/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.669Z","updated_at":"2025-05-22T16:37:21.669Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/kalign/align/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/learnmsa/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.714Z","updated_at":"2025-05-22T16:37:21.714Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/learnmsa/align/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/multiqc/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.861Z","updated_at":"2025-05-22T16:37:21.861Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/multiqc/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/muscle5/super5/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.906Z","updated_at":"2025-05-22T16:37:21.906Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/muscle5/super5/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/tcoffee/align/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:21.967Z","updated_at":"2025-05-22T16:37:21.967Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/align/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/tcoffee/tcs/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:22.160Z","updated_at":"2025-05-22T16:37:22.160Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/tcs/environment.yml","dependencies":[]},{"ecosystem":"pypi","filepath":"modules/nf-core/untar/environment.yml","sha":null,"kind":"manifest","created_at":"2025-05-22T16:37:22.288Z","updated_at":"2025-05-22T16:37:22.288Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/untar/environment.yml","dependencies":[]},{"ecosystem":"actions","filepath":".github/workflows/ci_master.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:49:54.381Z","updated_at":"2025-05-08T13:49:54.381Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/ci_master.yml","dependencies":[{"id":23039101893,"package_name":"actions/checkout","ecosystem":"actions","requirements":"0ad4b8fadaa221de15dcec353f45205ec38ea70b","direct":true,"kind":"composite","optional":false},{"id":23039101894,"package_name":"nf-core/setup-nextflow","ecosystem":"actions","requirements":"v2","direct":true,"kind":"composite","optional":false},{"id":23039101895,"package_name":"eWaterCycle/setup-apptainer","ecosystem":"actions","requirements":"main","direct":true,"kind":"composite","optional":false},{"id":23039101903,"package_name":"conda-incubator/setup-miniconda","ecosystem":"actions","requirements":"a4260408e20b96e80095f42ff7f1a15b27dd94ca","direct":true,"kind":"composite","optional":false},{"id":23039101936,"package_name":"jlumbroso/free-disk-space","ecosystem":"actions","requirements":"54081f138730dfa15788a46383842cd2f914a1be","direct":true,"kind":"composite","optional":false},{"id":23039101937,"package_name":"actions/checkout","ecosystem":"actions","requirements":"11bd71901bbe5b1630ceea73d27597364c9af683","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"actions","filepath":".github/workflows/template_version_comment.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:49:59.998Z","updated_at":"2025-05-08T13:49:59.998Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/.github/workflows/template_version_comment.yml","dependencies":[{"id":23039101938,"package_name":"actions/checkout","ecosystem":"actions","requirements":"11bd71901bbe5b1630ceea73d27597364c9af683","direct":true,"kind":"composite","optional":false},{"id":23039101939,"package_name":"nichmor/minimal-read-yaml","ecosystem":"actions","requirements":"v0.0.2","direct":true,"kind":"composite","optional":false},{"id":23039101941,"package_name":"mshick/add-pr-comment","ecosystem":"actions","requirements":"b8f338c590a895d50bcbfa6c5859251edc8952fc","direct":true,"kind":"composite","optional":false}]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastavalidator/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:28.900Z","updated_at":"2025-05-08T13:50:28.900Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/fastavalidator/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/fastqc/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:28.950Z","updated_at":"2025-05-08T13:50:28.950Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/fastqc/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/foldmason/createdb/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:28.992Z","updated_at":"2025-05-08T13:50:28.992Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/foldmason/createdb/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/foldmason/easymsa/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.033Z","updated_at":"2025-05-08T13:50:29.033Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/foldmason/easymsa/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/foldmason/msa2lddtreport/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.075Z","updated_at":"2025-05-08T13:50:29.075Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/foldmason/msa2lddtreport/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/mafft/align/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.145Z","updated_at":"2025-05-08T13:50:29.145Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/mafft/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/mafft/guidetree/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.188Z","updated_at":"2025-05-08T13:50:29.188Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/mafft/guidetree/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/magus/align/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.230Z","updated_at":"2025-05-08T13:50:29.230Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/magus/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/mtmalign/align/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.272Z","updated_at":"2025-05-08T13:50:29.272Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/mtmalign/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/pigz/compress/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.335Z","updated_at":"2025-05-08T13:50:29.335Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/pigz/compress/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/pigz/uncompress/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.376Z","updated_at":"2025-05-08T13:50:29.376Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/pigz/uncompress/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/consensus/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.439Z","updated_at":"2025-05-08T13:50:29.439Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/consensus/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/extractfrompdb/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.481Z","updated_at":"2025-05-08T13:50:29.481Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/extractfrompdb/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/tcoffee/regressive/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.533Z","updated_at":"2025-05-08T13:50:29.533Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/tcoffee/regressive/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"modules/nf-core/upp/align/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.608Z","updated_at":"2025-05-08T13:50:29.608Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/modules/nf-core/upp/align/meta.yml","dependencies":[]},{"ecosystem":"cpan","filepath":"subworkflows/nf-core/utils_nfschema_plugin/meta.yml","sha":null,"kind":"manifest","created_at":"2025-05-08T13:50:29.670Z","updated_at":"2025-05-08T13:50:29.670Z","repository_link":"https://github.com/nf-core/multiplesequencealign/blob/master/subworkflows/nf-core/utils_nfschema_plugin/meta.yml","dependencies":[]}],"score":null,"created_at":"2025-09-04T15:51:13.741Z","updated_at":"2025-10-07T08:16:10.786Z","avatar_url":"https://github.com/nf-core.png","language":"Nextflow","category":null,"sub_category":null,"monthly_downloads":0,"funding_links":[],"readme_doi_urls":["https://doi.org/10.5281/zenodo.13889386","https://dx.doi.org/10.1038/s41587-020-0439-x"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://science.ecosyste.ms/api/v1/projects/39448","html_url":"https://science.ecosyste.ms/projects/39448","bibtex_url":"https://science.ecosyste.ms/projects/39448/export.bibtex","apalike_url":"https://science.ecosyste.ms/projects/39448/export.apalike"}