{"id":"https://openalex.org/W4412454182","doi":"https://doi.org/10.1093/bioinformatics/btaf212","title":"Ultrafast and ultralarge multiple sequence alignments using TWILIGHT","display_name":"Ultrafast and ultralarge multiple sequence alignments using TWILIGHT","publication_year":2025,"publication_date":"2025-07-01","ids":{"openalex":"https://openalex.org/W4412454182","doi":"https://doi.org/10.1093/bioinformatics/btaf212","pmid":"https://pubmed.ncbi.nlm.nih.gov/40662833"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i332/63745685/btaf212.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i332/63745685/btaf212.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Yu-Hsiang Tseng","orcid":"https://orcid.org/0009-0005-8758-9739"},"institutions":[{"id":"https://openalex.org/I160856358","display_name":"University of San Diego","ror":"https://ror.org/03jbbze48","country_code":"US","type":"education","lineage":["https://openalex.org/I160856358"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yu-Hsiang Tseng","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California San Diego , San Diego, CA 92093,"],"raw_orcid":"https://orcid.org/0009-0005-8758-9739","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California San Diego , San Diego, CA 92093,","institution_ids":["https://openalex.org/I160856358","https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080633519","display_name":"Sumit Walia","orcid":"https://orcid.org/0000-0003-4557-2339"},"institutions":[{"id":"https://openalex.org/I160856358","display_name":"University of San Diego","ror":"https://ror.org/03jbbze48","country_code":"US","type":"education","lineage":["https://openalex.org/I160856358"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sumit Walia","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California San Diego , San Diego, CA 92093,"],"raw_orcid":"https://orcid.org/0000-0003-4557-2339","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California San Diego , San Diego, CA 92093,","institution_ids":["https://openalex.org/I160856358","https://openalex.org/I36258959"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5080797757","display_name":"Yatish Turakhia","orcid":"https://orcid.org/0000-0001-5600-2900"},"institutions":[{"id":"https://openalex.org/I160856358","display_name":"University of San Diego","ror":"https://ror.org/03jbbze48","country_code":"US","type":"education","lineage":["https://openalex.org/I160856358"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yatish Turakhia","raw_affiliation_strings":["Department of Electrical and Computer Engineering, University of California San Diego , San Diego, CA 92093,"],"raw_orcid":"https://orcid.org/0000-0001-5600-2900","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering, University of California San Diego , San Diego, CA 92093,","institution_ids":["https://openalex.org/I160856358","https://openalex.org/I36258959"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.5988,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.90043981,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"41","issue":"Supplement_1","first_page":"i332","last_page":"i341"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9592999815940857,"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":0.9592999815940857,"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/T11048","display_name":"Bacteriophages and microbial interactions","score":0.007899999618530273,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12946","display_name":"Fractal and DNA sequence analysis","score":0.006399999838322401,"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/twilight","display_name":"Twilight","score":0.8402888178825378},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8194052577018738},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7850691080093384},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5832235217094421},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.5630673170089722},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.5097317099571228},{"id":"https://openalex.org/keywords/throughput","display_name":"Throughput","score":0.4888541102409363},{"id":"https://openalex.org/keywords/parallelism","display_name":"Parallelism (grammar)","score":0.4510667622089386},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.4285615086555481},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.3277735710144043},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19522160291671753},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11489048600196838},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.09273719787597656}],"concepts":[{"id":"https://openalex.org/C2777298776","wikidata":"https://www.wikidata.org/wiki/Q164160","display_name":"Twilight","level":2,"score":0.8402888178825378},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8194052577018738},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7850691080093384},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5832235217094421},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.5630673170089722},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5097317099571228},{"id":"https://openalex.org/C157764524","wikidata":"https://www.wikidata.org/wiki/Q1383412","display_name":"Throughput","level":3,"score":0.4888541102409363},{"id":"https://openalex.org/C2781172179","wikidata":"https://www.wikidata.org/wiki/Q853109","display_name":"Parallelism (grammar)","level":2,"score":0.4510667622089386},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.4285615086555481},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.3277735710144043},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19522160291671753},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11489048600196838},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.09273719787597656},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","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},{"id":"https://openalex.org/C555944384","wikidata":"https://www.wikidata.org/wiki/Q249","display_name":"Wireless","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btaf212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i332/63745685/btaf212.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40662833","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40662833","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:ark:/13030/qt7t03z92g","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7t03z92g","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7t03z92g","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol 41, iss Supplement_1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12261412","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12261412","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf212","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf212","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/41/Supplement_1/i332/63745685/btaf212.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412454182.pdf","grobid_xml":"https://content.openalex.org/works/W4412454182.grobid-xml"},"referenced_works_count":57,"referenced_works":["https://openalex.org/W1748508858","https://openalex.org/W1969051510","https://openalex.org/W1969153299","https://openalex.org/W1975001431","https://openalex.org/W1982716005","https://openalex.org/W2031611770","https://openalex.org/W2055666215","https://openalex.org/W2056251063","https://openalex.org/W2060425093","https://openalex.org/W2068448872","https://openalex.org/W2074231493","https://openalex.org/W2097706568","https://openalex.org/W2102502076","https://openalex.org/W2106882534","https://openalex.org/W2127322768","https://openalex.org/W2127520112","https://openalex.org/W2127774996","https://openalex.org/W2132926880","https://openalex.org/W2135621733","https://openalex.org/W2137597742","https://openalex.org/W2144362290","https://openalex.org/W2147461064","https://openalex.org/W2155237411","https://openalex.org/W2159638180","https://openalex.org/W2160378127","https://openalex.org/W2168696662","https://openalex.org/W2521298622","https://openalex.org/W2575750030","https://openalex.org/W2796046773","https://openalex.org/W2950897217","https://openalex.org/W2991142785","https://openalex.org/W2994645871","https://openalex.org/W3005235420","https://openalex.org/W3025857586","https://openalex.org/W3081341939","https://openalex.org/W3092136311","https://openalex.org/W3109134151","https://openalex.org/W3156220950","https://openalex.org/W3177828909","https://openalex.org/W3196426464","https://openalex.org/W3204504530","https://openalex.org/W4213202832","https://openalex.org/W4247111930","https://openalex.org/W4254502766","https://openalex.org/W4255659575","https://openalex.org/W4281689324","https://openalex.org/W4289313383","https://openalex.org/W4293116279","https://openalex.org/W4309191898","https://openalex.org/W4363675392","https://openalex.org/W4377019635","https://openalex.org/W4386356042","https://openalex.org/W4386624280","https://openalex.org/W6644175424","https://openalex.org/W6674647444","https://openalex.org/W6680215730","https://openalex.org/W6808791420"],"related_works":["https://openalex.org/W2341012202","https://openalex.org/W2058965144","https://openalex.org/W2164382479","https://openalex.org/W2146343568","https://openalex.org/W98480971","https://openalex.org/W2150291671","https://openalex.org/W2013643406","https://openalex.org/W3138386522","https://openalex.org/W2499279132","https://openalex.org/W2076915000"],"abstract_inverted_index":{"MOTIVATION:":[0],"Multiple":[1],"sequence":[2],"alignment":[3,138,174,200],"(MSA)":[4],"is":[5,29,154,183],"a":[6,76,168],"fundamental":[7],"operation":[8],"in":[9,123],"bioinformatics,":[10],"yet":[11],"existing":[12,133],"MSA":[13,38,78],"tools":[14,39,122,134],"are":[15,206],"struggling":[16],"to":[17,54,104,158],"keep":[18],"up":[19],"with":[20,88],"the":[21,31,57,130,155,187],"speed":[22,110,124],"and":[23,33,50,63,69,85,91,98,125,135,175,195],"volume":[24],"of":[25,36,46,132,139,151,201],"incoming":[26],"data.":[27],"This":[28],"because":[30],"runtimes":[32],"memory":[34,86],"requirements":[35],"current":[37],"become":[40],"untenable":[41],"when":[42],"processing":[43],"large":[44],"numbers":[45],"long":[47],"input":[48],"sequences,":[49,166,205],"they":[51],"also":[52],"fail":[53],"fully":[55],"harness":[56],"parallelism":[58],"provided":[59],"by":[60],"modern":[61],"CPUs":[62],"GPUs.":[64],"RESULTS:":[65],"We":[66],"present":[67],"Tall":[68],"Wide":[70],"Alignments":[71],"at":[72,108,190,208],"High":[73],"Throughput":[74],"(TWILIGHT),":[75],"novel":[77],"tool":[79,157],"optimized":[80],"for":[81,171],"speed,":[82],"accuracy,":[83],"scalability,":[84],"constraints,":[87],"both":[89],"CPU":[90],"GPU":[92],"support.":[93],"TWILIGHT":[94,118,153],"incorporates":[95],"innovative":[96],"parallelization":[97],"memory-efficiency":[99],"strategies":[100],"that":[101],"enable":[102],"it":[103],"build":[105],"ultralarge":[106],"alignments":[107],"high":[109],"even":[111],"on":[112],"memory-constrained":[113],"devices.":[114],"On":[115],"challenging":[116],"datasets,":[117],"outperformed":[119],"all":[120],"other":[121],"accuracy.":[126],"It":[127],"scaled":[128],"beyond":[129],"limits":[131],"performed":[136],"an":[137],"1":[140],"million":[141,162,203],"RNASim":[142],"sequences":[143],"within":[144],"30":[145],"min":[146],"while":[147],"utilizing":[148],"<16":[149],"GB":[150],"memory.":[152],"first":[156],"align":[159],"over":[160],"8":[161,202],"publicly":[163],"available":[164,185,207],"SARS-CoV-2":[165,204],"setting":[167],"new":[169],"standard":[170],"large-scale":[172],"genomic":[173],"data":[176],"analysis.":[177],"AVAILABILITY":[178],"AND":[179],"IMPLEMENTATION:":[180],"TWILIGHT's":[181],"code":[182],"freely":[184],"under":[186],"MIT":[188],"license":[189],"https://github.com/TurakhiaLab/TWILIGHT.":[191],"The":[192],"test":[193],"datasets":[194],"experimental":[196],"results,":[197],"including":[198],"our":[199],"https://zenodo.org/records/14722035.":[209]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-16T13:24:37.021932","created_date":"2025-10-10T00:00:00"}
