{"id":"https://openalex.org/W7212363300","doi":"https://doi.org/10.64898/2026.09.10.750728","title":"Real-time accessible phylogenetics for every highly sampled virus","display_name":"Real-time accessible phylogenetics for every highly sampled virus","publication_year":2026,"publication_date":"2026-09-11","ids":{"openalex":"https://openalex.org/W7212363300","doi":"https://doi.org/10.64898/2026.09.10.750728"},"language":"en","primary_location":{"id":"doi:10.64898/2026.09.10.750728","doi":"https://doi.org/10.64898/2026.09.10.750728","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.750728","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.10.750728.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.10.750728.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031905987","display_name":"Angie S. Hinrichs","orcid":"https://orcid.org/0000-0002-1697-1130","observed_orcids":["https://orcid.org/0000-0002-1697-1130"]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Angie Hinrichs","raw_affiliation_strings":["Genomics institute, University of California, Santa Cruz. Santa Cruz, CA 95064"],"raw_orcid":"https://orcid.org/0000-0002-1697-1130","affiliations":[{"raw_affiliation_string":"Genomics institute, University of California, Santa Cruz. Santa Cruz, CA 95064","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095964485","display_name":"Lily Karim","orcid":"https://orcid.org/0000-0002-4972-7513","observed_orcids":["https://orcid.org/0000-0002-4972-7513"]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lily Karim","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064","Genomics institute, University of California, Santa Cruz. Santa Cruz, CA 95064"],"raw_orcid":"https://orcid.org/0000-0002-4972-7513","affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics institute, University of California, Santa Cruz. Santa Cruz, CA 95064","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080797757","display_name":"Yatish Turakhia","orcid":"https://orcid.org/0000-0001-5600-2900","observed_orcids":["https://orcid.org/0000-0001-5600-2900"]},"institutions":[{"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, USA"],"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, USA","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003694430","display_name":"Theo Sanderson","orcid":"https://orcid.org/0000-0003-4177-2851","observed_orcids":["https://orcid.org/0000-0003-4177-2851"]},"institutions":[{"id":"https://openalex.org/I4210089966","display_name":"London School of Hygiene & Tropical Medicine","ror":"https://ror.org/00a0jsq62","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I4210089966"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Theo Sanderson","raw_affiliation_strings":["London School of Hygiene and Tropical Medicine, London, England, UK"],"raw_orcid":"https://orcid.org/0000-0003-4177-2851","affiliations":[{"raw_affiliation_string":"London School of Hygiene and Tropical Medicine, London, England, UK","institution_ids":["https://openalex.org/I4210089966"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5076593250","display_name":"Russell B Corbett-Detig","orcid":"https://orcid.org/0000-0001-6535-2478","observed_orcids":["https://orcid.org/0000-0001-6535-2478"]},"institutions":[{"id":"https://openalex.org/I185103710","display_name":"University of California, Santa Cruz","ror":"https://ror.org/03s65by71","country_code":"US","type":"education","lineage":["https://openalex.org/I185103710"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Russ Corbett-Detig","raw_affiliation_strings":["Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064","Genomics institute, University of California, Santa Cruz. Santa Cruz, CA 95064"],"raw_orcid":"https://orcid.org/0000-0001-6535-2478","affiliations":[{"raw_affiliation_string":"Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, 95064","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics institute, University of California, Santa Cruz. Santa Cruz, CA 95064","institution_ids":["https://openalex.org/I185103710"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003694430"],"corresponding_institution_ids":["https://openalex.org/I4210089966"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9940999746322632,"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":0.9940999746322632,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.003100000089034438,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/T10118","display_name":"SARS-CoV-2 and COVID-19 Research","score":0.0003000000142492354,"subfield":{"id":"https://openalex.org/subfields/2725","display_name":"Infectious Diseases"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/viral-phylogeny","display_name":"viral phylogeny","score":0.9900000095367432},{"id":"https://openalex.org/keywords/usher","display_name":"ushers","score":0.8949999809265137},{"id":"https://openalex.org/keywords/mutation-spectrum","display_name":"mutation spectrum","score":0.492000013589859},{"id":"https://openalex.org/keywords/baltimore-classification","display_name":"Baltimore classification","score":0.7149999737739563},{"id":"https://openalex.org/keywords/viral-replication-machinery","display_name":"viral replication machinery","score":0.8309999704360962},{"id":"https://openalex.org/keywords/genomic-epidemiology","display_name":"genomic epidemiology","score":0.7400000095367432},{"id":"https://openalex.org/keywords/phylogenetic-placement","display_name":"phylogenetic placement","score":0.7979999780654907},{"id":"https://openalex.org/keywords/viral-genome-sequence","display_name":"viral genome sequence","score":0.45100000500679016},{"id":"https://openalex.org/keywords/viral-evolution","display_name":"viral evolution","score":0.5059999823570251},{"id":"https://openalex.org/keywords/covid-19","display_name":"COVID-19 pandemic","score":0.5400000214576721}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6952000260353088},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6403999924659729},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6302000284194946},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6152999997138977},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.529699981212616},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5001000165939331},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.49000000953674316},{"id":"https://openalex.org/C124388736","wikidata":"https://www.wikidata.org/wiki/Q3247497","display_name":"Tree of life (biology)","level":4,"score":0.43650001287460327},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.421999990940094},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4043000042438507},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.38960000872612},{"id":"https://openalex.org/C8769409","wikidata":"https://www.wikidata.org/wiki/Q2066554","display_name":"Viral evolution","level":4,"score":0.3822000026702881},{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.3765000104904175},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3610999882221222},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.3449999988079071},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.3273000121116638},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.3068000078201294},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3043999969959259},{"id":"https://openalex.org/C12590798","wikidata":"https://www.wikidata.org/wiki/Q3933199","display_name":"Replication (statistics)","level":2,"score":0.2903999984264374},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.28189998865127563},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.2773999869823456},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.27309998869895935},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.27219998836517334},{"id":"https://openalex.org/C41584329","wikidata":"https://www.wikidata.org/wiki/Q175902","display_name":"Sequence database","level":3,"score":0.2718000113964081},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2653999924659729},{"id":"https://openalex.org/C18949551","wikidata":"https://www.wikidata.org/wiki/Q740578","display_name":"Sequence assembly","level":5,"score":0.2635999917984009},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.2551000118255615},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.25360000133514404},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.25099998712539673}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.64898/2026.09.10.750728","doi":"https://doi.org/10.64898/2026.09.10.750728","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.750728","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.10.750728.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.64898/2026.09.10.750728","doi":"https://doi.org/10.64898/2026.09.10.750728","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.09.10.750728","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2026/09/11/2026.09.10.750728.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1367180378","display_name":null,"funder_award_id":"75D30124C20302","funder_id":"https://openalex.org/F4320332162","funder_display_name":"Centers for Disease Control and Prevention"},{"id":"https://openalex.org/G6039271873","display_name":"Viral genomic surveillance in the era of million-sequence trees","funder_award_id":"306920/Z/23/Z","funder_id":"https://openalex.org/F4320311904","funder_display_name":"Wellcome Trust"}],"funders":[{"id":"https://openalex.org/F4320311904","display_name":"Wellcome Trust","ror":"https://ror.org/029chgv08"},{"id":"https://openalex.org/F4320332162","display_name":"Centers for Disease Control and Prevention","ror":"https://ror.org/042twtr12"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7212363300.pdf","grobid_xml":"https://content.openalex.org/works/W7212363300.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W1981572321","https://openalex.org/W2088481129","https://openalex.org/W2101797035","https://openalex.org/W2104998102","https://openalex.org/W2108982334","https://openalex.org/W2110335151","https://openalex.org/W2114850508","https://openalex.org/W2114938008","https://openalex.org/W2118327902","https://openalex.org/W2136847298","https://openalex.org/W2142773663","https://openalex.org/W2171202548","https://openalex.org/W2904250115","https://openalex.org/W2951878836","https://openalex.org/W2997069256","https://openalex.org/W3009335848","https://openalex.org/W3035786310","https://openalex.org/W3043177992","https://openalex.org/W3118497926","https://openalex.org/W3158098632","https://openalex.org/W3160568774","https://openalex.org/W3187962553","https://openalex.org/W3196426464","https://openalex.org/W3215610096","https://openalex.org/W4283321093","https://openalex.org/W4291016578","https://openalex.org/W4294612836","https://openalex.org/W4306941746","https://openalex.org/W4308963287","https://openalex.org/W4310490448","https://openalex.org/W4363675392","https://openalex.org/W4376641786","https://openalex.org/W4390345660","https://openalex.org/W4391215307","https://openalex.org/W4391539704","https://openalex.org/W4400353742","https://openalex.org/W4406521338","https://openalex.org/W4408566819","https://openalex.org/W4412093882","https://openalex.org/W7170072349","https://openalex.org/W7213428392","https://openalex.org/W7223227188"],"related_works":["https://openalex.org/W4200400262","https://openalex.org/W3160568774","https://openalex.org/W2951878836","https://openalex.org/W4308963287","https://openalex.org/W3209690221","https://openalex.org/W4408912933","https://openalex.org/W7051249515","https://openalex.org/W4417524457","https://openalex.org/W7117325601","https://openalex.org/W7213484558"],"abstract_inverted_index":{"Abstract":[0],"The":[1],"scale":[2],"of":[3,57,59,61,79,148,155,177],"viral":[4,31,85,149,163,182,210],"genome":[5],"sequencing":[6],"has":[7],"outpaced":[8],"the":[9,20,68,137,140,146,153,178],"phylogenetic":[10,108],"tools":[11],"traditionally":[12],"used":[13],"to":[14],"analyze":[15],"it,":[16],"as":[17,90,172],"highlighted":[18],"by":[19,136,158],"COVID-19":[21],"pandemic.":[22],"We":[23,95,151,166],"present":[24],"viral_usher,":[25],"a":[26,38,77,99,103],"unified":[27],"framework":[28],"for":[29,200,205],"scalable":[30],"phylogenetics":[32],"built":[33,135],"on":[34],"UShER.":[35],"viral_usher":[36],"is":[37,134],"containerized":[39],"command-line":[40],"tool":[41],"that":[42,116,168],"constructs":[43],"mutation-annotated":[44],"trees":[45],"directly":[46],"from":[47,98],"public":[48],"sequence":[49],"repositories":[50],"with":[51],"minimal":[52],"user":[53],"input,":[54],"building":[55],"phylogenies":[56,81,126],"tens":[58],"thousands":[60],"genomes":[62,92],"in":[63],"minutes.":[64],"Applying":[65],"it":[66],"across":[67,145,180,209],"International":[69],"Nucleotide":[70],"Sequence":[71],"Database":[72],"Collaboration,":[73],"we":[74],"assembled":[75],"viral_usher_trees,":[76],"repository":[78,141],"446":[80],"spanning":[82],"163":[83],"well-sequenced":[84],"species,":[86],"rebuilt":[87],"automatically":[88],"monthly":[89],"new":[91],"are":[93,215],"deposited.":[94],"extended":[96],"Taxonium":[97],"tree":[100,113,133],"viewer":[101],"into":[102],"web":[104],"platform":[105,199],"supporting":[106],"in-browser":[107],"placement":[109],"and":[110,121,187,204,213,225],"de":[111],"novo":[112],"construction,":[114],"so":[115],"users":[117],"can":[118],"upload":[119],"sequences":[120],"contextualize":[122],"them":[123],"within":[124],"global":[125],"without":[127],"local":[128],"computational":[129],"infrastructure.":[130],"Because":[131],"every":[132],"same":[138],"procedure,":[139],"enables":[142],"comparative":[143,206],"analyses":[144],"breadth":[147],"diversity.":[150],"demonstrate":[152],"utility":[154],"this":[156],"resource":[157],"asking":[159],"what":[160],"factors":[161],"shape":[162],"mutation":[164],"spectra.":[165],"found":[167],"replication":[169],"machinery,":[170],"captured":[171],"Baltimore":[173],"class,":[174],"explains":[175],"46%":[176],"variance":[179],"162":[181],"genomes,":[183],"while":[184],"host":[185],"taxon":[186],"envelope":[188],"status":[189],"together":[190],"explain":[191],"under":[192],"5%.":[193],"These":[194],"resources":[195],"provide":[196],"an":[197],"extensible":[198],"real-time":[201],"genomic":[202],"epidemiology":[203],"evolutionary":[207],"analysis":[208],"pathogens.":[211],"Resources":[212],"code":[214],"freely":[216],"available":[217],"at":[218],"https://taxonium.org/":[219],",":[220,222,224],"https://github.com/lilymaryam/spectrum_analysis":[221],"https://github.com/AngieHinrichs/viral_usher_trees":[223],"https://github.com/AngieHinrichs/viral_usher":[226],".":[227]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-09-13T00:00:00"}
