{"doi":"10.1093/nar/gkh340","title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","abstract":"We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the log-expectation score, and refinement using tree-dependent restricted partitioning. The speed and accuracy of MUSCLE are compared with T-Coffee, MAFFT and CLUSTALW on four test sets of reference alignments: BAliBASE, SABmark, SMART and a new benchmark, PREFAB. MUSCLE achieves the highest, or joint highest, rank in accuracy on each of these sets. Without refinement, MUSCLE achieves average accuracy statistically indistinguishable from T-Coffee and MAFFT, and is the fastest of the tested methods for large numbers of sequences, aligning 5000 sequences of average length 350 in 7 min on a current desktop computer. The MUSCLE program, source code and PREFAB test data are freely available at http://www.drive5. com/muscle.","journal":"Nucleic Acids Research","year":2004,"id":7959,"datarank":29.900100887455295,"base_score":10.739890564725489,"endowment":10.739890564725489,"self_citation_contribution":1.6109835847088234,"citation_network_contribution":28.289117302746472,"self_endowment_contribution":1.6109835847088234,"citer_contribution":28.289117302746472,"corpus_percentile":99.7,"corpus_rank":89,"citation_count":46160,"citer_count":196,"citers_with_citation_signal":196,"citers_with_endowment":196,"datacite_reuse_total":0,"is_dataset":false,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2004-03-08","authors":[{"id":29074,"name":"R. C. Edgar","orcid":"0000-0001-7355-2541","position":0,"is_corresponding":true}],"reference_count":46,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-03-01T18:20:47.508186Z","pmid":null,"pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}