{"id":"https://openalex.org/W4254895086","doi":"https://doi.org/10.1109/csb.2004.1332560","title":"MUSCLE: multiple sequence alignment with improved accuracy and speed","display_name":"MUSCLE: multiple sequence alignment with improved accuracy and speed","publication_year":2004,"publication_date":"2004-11-08","ids":{"openalex":"https://openalex.org/W4254895086","doi":"https://doi.org/10.1109/csb.2004.1332560"},"language":"en","primary_location":{"id":"doi:10.1109/csb.2004.1332560","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332560","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":"1752-7791","issn":["1752-7791"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077667471","display_name":"R. C. Edgar","orcid":"https://orcid.org/0000-0001-7355-2541"},"institutions":[{"id":"https://openalex.org/I95457486","display_name":"University of California, Berkeley","ror":"https://ror.org/01an7q238","country_code":"US","type":"education","lineage":["https://openalex.org/I95457486"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"R.C. Edgar","raw_affiliation_strings":["Department of Plant and Microbial Biology, University of California, Berkeley, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant and Microbial Biology, University of California, Berkeley, USA","institution_ids":["https://openalex.org/I95457486"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5077667471"],"corresponding_institution_ids":["https://openalex.org/I95457486"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":42,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"689","last_page":"690"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9973000288009644,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9926000237464905,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7280657291412354},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.5796760320663452},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.5408473610877991},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.47238588333129883},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4611722528934479},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3429713547229767},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.32163935899734497},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.09722450375556946},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07517755031585693}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7280657291412354},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.5796760320663452},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.5408473610877991},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.47238588333129883},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4611722528934479},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3429713547229767},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.32163935899734497},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.09722450375556946},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07517755031585693},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/csb.2004.1332560","is_oa":false,"landing_page_url":"https://doi.org/10.1109/csb.2004.1332560","pdf_url":null,"source":{"id":"https://openalex.org/S4363608884","display_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","issn_l":"1752-7791","issn":["1752-7791"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1969153299","https://openalex.org/W1996681309","https://openalex.org/W2006290495","https://openalex.org/W2106882534","https://openalex.org/W2109607376","https://openalex.org/W2126332379","https://openalex.org/W2128613007","https://openalex.org/W2132926880","https://openalex.org/W2144362290","https://openalex.org/W2147285856","https://openalex.org/W2148311769","https://openalex.org/W3012079654"],"related_works":["https://openalex.org/W2317245370","https://openalex.org/W2076915000","https://openalex.org/W4249323025","https://openalex.org/W198851386","https://openalex.org/W2030310580","https://openalex.org/W947442053","https://openalex.org/W1980160788","https://openalex.org/W2148915962","https://openalex.org/W2283866686","https://openalex.org/W2143599190"],"abstract_inverted_index":{"We":[0],"present":[1],"MUSCLE,":[2],"a":[3,89],"new":[4],"program":[5],"for":[6,48,55,72],"creating":[7],"multiple":[8],"alignments":[9],"of":[10,75,82],"protein":[11],"sequences.":[12],"MUSCLE":[13,58,92],"achieves":[14],"the":[15,68],"highest":[16],"scores":[17],"so":[18],"far":[19],"reported":[20],"on":[21,88],"four":[22],"alignment":[23],"benchmarks:":[24],"Balibase,":[25],"PREFAB,":[26],"SABmark":[27],"and":[28,39,66],"SMART,":[29],"achieving":[30],"accuracy":[31,61],"from":[32,64],"1%":[33],"to":[34,78],"2.5%":[35],"higher":[36],"than":[37,46],"T-Coffee":[38,65],"execution":[40],"times":[41],"that":[42],"are":[43],"generally":[44],"lower":[45],"CLUSTALW":[47],"typical":[49],"input":[50],"data.":[51],"With":[52],"options":[53],"designed":[54],"high-throughput":[56],"applications,":[57],"gives":[59],"average":[60],"statistically":[62],"indistinguishable":[63],"is":[67,93],"fastest":[69],"published":[70],"method":[71],"large":[73],"numbers":[74],"sequences,":[76],"able":[77],"align":[79],"5,000":[80],"sequences":[81],"length":[83],"300":[84],"in":[85],"7":[86],"minutes":[87],"desktop":[90],"computer.":[91],"freely":[94],"available":[95],"at":[96],"http://www.drive5.com/muscle.":[97]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2025-10-10T00:00:00"}
