{"id":"https://openalex.org/W4416649878","doi":"https://doi.org/10.1371/journal.pcbi.1013676","title":"T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters","display_name":"T-shaped alignments integrating HIV-1 near full-length genome and partial pol sequences can improve phylogenetic inference of transmission clusters","publication_year":2025,"publication_date":"2025-11-25","ids":{"openalex":"https://openalex.org/W4416649878","doi":"https://doi.org/10.1371/journal.pcbi.1013676","pmid":"https://pubmed.ncbi.nlm.nih.gov/41289307"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013676","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013676","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1013676","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013035310","display_name":"August Guang","orcid":"https://orcid.org/0000-0003-4974-1873"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"August Guang","raw_affiliation_strings":["Center for Computation and Visualization, Brown University, Providence, Rhode Island, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-4974-1873","affiliations":[{"raw_affiliation_string":"Center for Computation and Visualization, Brown University, Providence, Rhode Island, United States of America","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068691883","display_name":"Casey W. Dunn","orcid":"https://orcid.org/0000-0003-0628-5150"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Casey W Dunn","raw_affiliation_strings":["Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America"],"raw_orcid":"https://orcid.org/0000-0003-0628-5150","affiliations":[{"raw_affiliation_string":"Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, United States of America","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087165714","display_name":"Vladimir Novitsky","orcid":"https://orcid.org/0000-0002-4279-9071"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Vlad Novitsky","raw_affiliation_strings":["Warren Alpert Medical School, Brown University, Providence, Rhode Island, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Warren Alpert Medical School, Brown University, Providence, Rhode Island, United States of America","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036886045","display_name":"Mark Howison","orcid":"https://orcid.org/0000-0002-0764-4090"},"institutions":[{"id":"https://openalex.org/I53118340","display_name":"Rhode Island College","ror":"https://ror.org/01k5gt570","country_code":"US","type":"education","lineage":["https://openalex.org/I53118340"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Howison","raw_affiliation_strings":["Research Improving Peoples' Lives, Providence, Rhode Island, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Research Improving Peoples' Lives, Providence, Rhode Island, United States of America","institution_ids":["https://openalex.org/I53118340"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051239322","display_name":"Rami Kantor","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Rami Kantor","raw_affiliation_strings":["Warren Alpert Medical School, Brown University, Providence, Rhode Island, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Warren Alpert Medical School, Brown University, Providence, Rhode Island, United States of America","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5013035310","https://openalex.org/A5036886045","https://openalex.org/A5051239322","https://openalex.org/A5068691883","https://openalex.org/A5087165714"],"corresponding_institution_ids":["https://openalex.org/I27804330","https://openalex.org/I32971472","https://openalex.org/I53118340"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.26957829,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"21","issue":"11","first_page":"e1013676","last_page":"e1013676"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.6373000144958496,"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":0.6373000144958496,"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/T10112","display_name":"HIV Research and Treatment","score":0.23680000007152557,"subfield":{"id":"https://openalex.org/subfields/2406","display_name":"Virology"},"field":{"id":"https://openalex.org/fields/24","display_name":"Immunology and Microbiology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.03519999980926514,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8385999798774719},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7008000016212463},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6791999936103821},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5432999730110168},{"id":"https://openalex.org/keywords/cluster","display_name":"Cluster (spacecraft)","score":0.5360999703407288},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5259000062942505},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5030999779701233},{"id":"https://openalex.org/keywords/transmission","display_name":"Transmission (telecommunications)","score":0.44940000772476196},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.41830000281333923}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8385999798774719},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7008000016212463},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6791999936103821},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5432999730110168},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5386000275611877},{"id":"https://openalex.org/C164866538","wikidata":"https://www.wikidata.org/wiki/Q367351","display_name":"Cluster (spacecraft)","level":2,"score":0.5360999703407288},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5259000062942505},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5123999714851379},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5030999779701233},{"id":"https://openalex.org/C761482","wikidata":"https://www.wikidata.org/wiki/Q118093","display_name":"Transmission (telecommunications)","level":2,"score":0.44940000772476196},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4341000020503998},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.41830000281333923},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.4083000123500824},{"id":"https://openalex.org/C3013748606","wikidata":"https://www.wikidata.org/wiki/Q15787","display_name":"Human immunodeficiency virus (HIV)","level":2,"score":0.38530001044273376},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.3603000044822693},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.3447999954223633},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.3395000100135803},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3393999934196472},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.3287999927997589},{"id":"https://openalex.org/C196662502","wikidata":"https://www.wikidata.org/wiki/Q827541","display_name":"Molecular clock","level":4,"score":0.3237000107765198},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3100999891757965},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.30820000171661377},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3000999987125397},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.27639999985694885},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27320000529289246},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.25999999046325684},{"id":"https://openalex.org/C166393388","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Molecular evolution","level":4,"score":0.2587999999523163},{"id":"https://openalex.org/C195239911","wikidata":"https://www.wikidata.org/wiki/Q2007033","display_name":"Molecular phylogenetics","level":4,"score":0.2583000063896179},{"id":"https://openalex.org/C134261354","wikidata":"https://www.wikidata.org/wiki/Q938438","display_name":"Statistical inference","level":2,"score":0.2522999942302704}],"mesh":[{"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015497","descriptor_name":"HIV-1","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000453","qualifier_name":"epidemiology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000635","qualifier_name":"transmission","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D015658","descriptor_name":"HIV Infections","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":true},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1013676","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013676","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:41289307","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41289307","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:c4f0484adeab4afbb8943c5fc7b8df22","is_oa":true,"landing_page_url":"https://doaj.org/article/c4f0484adeab4afbb8943c5fc7b8df22","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"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":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 21, Iss 11, p e1013676 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12685204","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12685204/","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013676","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013676","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G300478360","display_name":null,"funder_award_id":"K24AI134359","funder_id":"https://openalex.org/F4320309123","funder_display_name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3505326821","display_name":null,"funder_award_id":"K24 AI134359","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G3926767023","display_name":null,"funder_award_id":"P20GM109035","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4760462093","display_name":null,"funder_award_id":"P20 GM109035","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G5946963666","display_name":null,"funder_award_id":"RO1AI136058","funder_id":"https://openalex.org/F4320338412","funder_display_name":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6121298687","display_name":null,"funder_award_id":"R01 AI136058","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G6290713876","display_name":null,"funder_award_id":"P30AI042853","funder_id":"https://openalex.org/F4320309123","funder_display_name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G7515270792","display_name":null,"funder_award_id":"P30 AI042853","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320309123","display_name":"Division of Intramural Research, National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320338412","display_name":"Division of Microbiology and Infectious Diseases, National Institute of Allergy and Infectious Diseases","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W24778476","https://openalex.org/W1966972227","https://openalex.org/W2010981336","https://openalex.org/W2052857100","https://openalex.org/W2060425093","https://openalex.org/W2078210212","https://openalex.org/W2101797035","https://openalex.org/W2111647009","https://openalex.org/W2113799994","https://openalex.org/W2119284380","https://openalex.org/W2136353610","https://openalex.org/W2328380983","https://openalex.org/W2494835558","https://openalex.org/W2566672496","https://openalex.org/W2598381200","https://openalex.org/W2915395120","https://openalex.org/W2934310577","https://openalex.org/W2952299127","https://openalex.org/W3009906763","https://openalex.org/W3032507263","https://openalex.org/W3039108403","https://openalex.org/W3048478224","https://openalex.org/W3095611768","https://openalex.org/W3103816374","https://openalex.org/W3165179933","https://openalex.org/W3193928773","https://openalex.org/W3212329743","https://openalex.org/W4200051093","https://openalex.org/W4213032483","https://openalex.org/W4213195146","https://openalex.org/W4310433486","https://openalex.org/W4313910035","https://openalex.org/W4317999660","https://openalex.org/W4387517028","https://openalex.org/W4400497278","https://openalex.org/W4403247716","https://openalex.org/W4404232274","https://openalex.org/W4407302425"],"related_works":[],"abstract_inverted_index":{"Molecular":[0],"epidemiology":[1],"and":[2,13,53,81,85,125,134,152,156,190,217,255,272],"HIV-1":[3,55,79,116,264],"transmission":[4,11],"networks":[5],"reconstruction":[6,92],"can":[7,27,57,269],"provide":[8],"insights":[9],"into":[10],"dynamics":[12],"inform":[14],"public":[15],"health":[16],"strategies.":[17],"Long":[18],"HIV":[19,46,63],"sequences,":[20,84],"such":[21],"as":[22],"near":[23],"full-length":[24],"(nFL)":[25],"genomes,":[26],"improve":[28,58,270,296],"the":[29,97,107,119,130,162,177,185,196,222,228,234],"accuracy":[30,199,208,238],"of":[31,51,61,93,103,132,172,214,230,266],"phylogenetic":[32,59,91,271,297],"inference.":[33],"However,":[34,194],"relatively":[35],"short":[36,54,135],"pol":[37,83],"sequences":[38,56,105,117,136,174,232,265,294],"are":[39,175],"still":[40],"broadly":[41],"used":[42],"for":[43,290],"inferring":[44],"molecular":[45,62,94],"clusters.":[47,95],"Whether":[48],"a":[49,69,126,243,287],"mix":[50,263],"long":[52,104,133],"inference":[60,158],"clusters":[64,192,215],"remains":[65],"unknown.":[66],"We":[67],"propose":[68],"flexible":[70],"approach":[71,89,254],"called":[72],"T-shaped":[73,178,235],"alignments":[74,261],"that":[75,99,167,227,258],"incorporates":[76],"both":[77],"nFL":[78,115,231,277],"genomes":[80],"partial":[82],"investigate":[86],"whether":[87],"this":[88],"improves":[90,237],"Under":[96],"assumption":[98],"clustering":[100,240,273],"from":[101,118],"100%":[102,186],"is":[106],"most":[108],"accurate,":[109],"we":[110,165,225],"obtained":[111],"1196":[112],"subtype":[113],"B":[114],"Los":[120],"Alamos":[121],"National":[122],"Laboratory":[123],"Database":[124],"single-study":[127],"subset,":[128],"varied":[129],"proportion":[131,278],"in":[137,149,239],"our":[138],"T-shape":[139,260,284],"alignments,":[140],"systematically":[141],"masked":[142],"all":[143,292],"non-pol":[144],"regions":[145],"with":[146,188,275],"missing":[147],"characters":[148],"proportional":[150],"increments,":[151],"compared":[153],"tree":[154],"similarity":[155],"cluster":[157,207,219],"among":[159],"datasets.":[160],"With":[161],"full":[163],"dataset,":[164,224],"found":[166,216,226],"when":[168],"more":[169,189],"than":[170],"50%":[171,197],"available":[173,293],"nFL,":[176],"alignment":[179,236,285],"gradually":[180],"yields":[181],"results":[182,256],"closer":[183],"to":[184,233,262,295],"n,":[187],"larger":[191],"identified.":[193],"below":[195],"threshold":[198,245],"did":[200],"not":[201],"increase.":[202],"Stringent":[203],"bootstrap":[204,250],"thresholds":[205],"decreased":[206,212],"gaps":[209],"but":[210],"also":[211],"number":[213],"mean":[218],"size.":[220],"For":[221],"subset":[223],"introduction":[229],"either":[241],"after":[242],"30%":[244],"or":[246],"immediately":[247],"depending":[248,279],"on":[249,280],"choice.":[251],"Our":[252],"new":[253],"suggest":[257],"using":[259],"different":[267],"lengths":[268],"accuracy,":[274],"needed":[276],"analysis":[281],"goals.":[282],"The":[283],"provides":[286],"straightforward":[288],"method":[289],"utilizing":[291],"analysis.":[298]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-11-25T00:00:00"}