{"id":17606523,"url":"https://github.com/mhahsler/rmsa","last_synced_at":"2026-01-08T16:06:02.743Z","repository":{"id":66161442,"uuid":"43763253","full_name":"mhahsler/rMSA","owner":"mhahsler","description":"Interface to Popular Multiple Sequence Alignment Tools - R-package","archived":false,"fork":false,"pushed_at":"2024-09-06T16:33:34.000Z","size":628,"stargazers_count":12,"open_issues_count":0,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-29T23:16:45.431Z","etag":null,"topics":["bioinformatics","sequence-alignment"],"latest_commit_sha":null,"homepage":"","language":"TeX","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mhahsler.png","metadata":{"files":{"readme":"README.Rmd","changelog":"NEWS.md","contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2015-10-06T16:31:10.000Z","updated_at":"2025-02-04T18:03:01.000Z","dependencies_parsed_at":"2024-09-06T19:10:05.885Z","dependency_job_id":"4ac91c56-bd3c-44d1-8b26-e02bba116c19","html_url":"https://github.com/mhahsler/rMSA","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/mhahsler/rMSA","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrMSA","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrMSA/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrMSA/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrMSA/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mhahsler","download_url":"https://codeload.github.com/mhahsler/rMSA/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mhahsler%2FrMSA/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28246679,"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":"2026-01-08T02:00:06.591Z","response_time":241,"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"}},"keywords":["bioinformatics","sequence-alignment"],"created_at":"2024-10-22T15:44:44.727Z","updated_at":"2026-01-08T16:06:02.715Z","avatar_url":"https://github.com/mhahsler.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"---\noutput: github_document\n---\n\n```{r echo=FALSE, results = 'asis'}\npkg \u003c- \"rMSA\"\n\nsource(\"https://raw.githubusercontent.com/mhahsler/pkg_helpers/main/pkg_helpers.R\")\npkg_title(pkg, CRAN = FALSE)\n```\n\n\nSeamlessly interfaces Multiple Sequence Alignment software packages including \n\n* ClustalW\n* MAFFT \n* MUSCLE\n* Kalign\n* Boxshade\n\nwith the Bioconductor infrastructure. The tools have to be installed separately.\n\nIn addition, distances between sets of sequences can be calculated providing.\n\n* k-mer-based distances\n  * Jensen-Shannon divergence (JSD) between FFPs (Sims and Kim, 2011)\n  * Cosine distance is used between Composition Vectors (Qi et al, 2007)\n  * Numerical summarization vector distance (Nagar and Hahsler, 2013)\n  * Jaccard distance between sets of k-mers.\n  * Distance based on SimRank (Santis et al, 2011)\n\n* Edit distance/alignment-based distances\n    * Edit (Levenshtein) Distance (package pwalign)\n    * Distance based on alignment scores (package pwalign)\n\n* Evolutionary distances\n    * Evolutionary distances (package ape)\n\nA short guide with examples can be found \n[here](http://github.com/mhahsler/rMSA/raw/master/vignettes_real/rMSA.pdf).\n\n```{r echo=FALSE, results = 'asis'}\npkg_install(pkg, CRAN = FALSE)\n```\n\nAdditional installation instructions can be found [here](INSTALL).\n\n\n## Examples\n\nAlign sequences using clustalW.\n\n```{r}\nlibrary(\"rMSA\")\n\nrna \u003c- readRNAStringSet(system.file(\"examples/RNA_example.fasta\", package = \"rMSA\"))\nrna\n\nal \u003c- clustal(rna)\nal\n```\nCluster mutations of a sequence using SimRank\n\n```{r}\ns \u003c- random_sequences(len = 100, number = 1)\nms \u003c- mutations(s, number = 20)\ndSimRank \u003c- distSimRank(ms)\nplot(as.dendrogram(hclust(dSimRank)), horiz=TRUE, type=\"triangle\")\n```\n\n# How to Cite the Use of this Package\n\n```{r echo=FALSE, results = 'asis'}\npkg_citation(pkg)\n```\n\n\n# References\n\nGao, L; Qi, J (2007 Mar 15). \"Whole genome molecular phylogeny of large dsDNA viruses using composition vector method.\". BMC evolutionary biology 7: 41. PMID 17359548.\n\nHahsler M, Nagar A (2024). _rMSA: Interface for Popular Multiple Sequence Alignment Tools_. R package version\n  0.99.1.\n\nAnurag Nagar; Michael Hahsler (2013). \"Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.\" BMC Bioinformatics, 14(Suppl. 11), 2013\n\nSantis et al, Simrank: Rapid and sensitive general-purpose k-mer search tool, BMC Ecology 2011, 11:11\n\nSims, GE; Kim, SH (2011 May 17). \"Whole-genome phylogeny of Escherichia coli/Shigella group by feature frequency profiles (FFPs).\". Proceedings of the National Academy of Sciences of the United States of America 108 (20): 8329-34. PMID 21536867.\n\nQi J, Wang B, Hao B: Whole Proteome Prokaryote Phylogeny without Sequence Alignment: A K-String Composition Approach. Journal of Molecular Evolution 2004, 58:1-11.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmhahsler%2Frmsa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmhahsler%2Frmsa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmhahsler%2Frmsa/lists"}