{"id":"https://openalex.org/W4386322170","doi":"https://doi.org/10.1093/bioinformatics/btad536","title":"DecentTree: scalable Neighbour-Joining for the genomic era","display_name":"DecentTree: scalable Neighbour-Joining for the genomic era","publication_year":2023,"publication_date":"2023-08-31","ids":{"openalex":"https://openalex.org/W4386322170","doi":"https://doi.org/10.1093/bioinformatics/btad536","pmid":"https://pubmed.ncbi.nlm.nih.gov/37651445"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad536","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad536","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad536/51316859/btad536.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/advance-article-pdf/doi/10.1093/bioinformatics/btad536/51316859/btad536.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030576317","display_name":"Weiwen Wang","orcid":"https://orcid.org/0000-0001-9319-450X"},"institutions":[{"id":"https://openalex.org/I4210149137","display_name":"China National GeneBank","ror":"https://ror.org/03n9hr695","country_code":"CN","type":"archive","lineage":["https://openalex.org/I4210149137"]},{"id":"https://openalex.org/I4387153646","display_name":"BGI Research","ror":"https://ror.org/05gsxrt27","country_code":"CN","type":"nonprofit","lineage":["https://openalex.org/I100135526","https://openalex.org/I4387153646"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiwen Wang","raw_affiliation_strings":["China National GeneBank, BGI Research , Shenzhen 518083, China","China National GeneBank, BGI Research, Shenzhen, 518083, China"],"raw_orcid":"https://orcid.org/0000-0001-9319-450X","affiliations":[{"raw_affiliation_string":"China National GeneBank, BGI Research , Shenzhen 518083, China","institution_ids":["https://openalex.org/I4210149137"]},{"raw_affiliation_string":"China National GeneBank, BGI Research, Shenzhen, 518083, China","institution_ids":["https://openalex.org/I4210149137","https://openalex.org/I4387153646"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077306639","display_name":"James Barbetti","orcid":null},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"James Barbetti","raw_affiliation_strings":["School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2601, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091416583","display_name":"Thomas K. F. Wong","orcid":"https://orcid.org/0000-0002-0580-6324"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Thomas Wong","raw_affiliation_strings":["Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2601, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063542140","display_name":"Bryan Thornlow","orcid":"https://orcid.org/0000-0001-6334-5186"},"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":"Bryan Thornlow","raw_affiliation_strings":["Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA 95064, United States","Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064, United States"],"raw_orcid":"https://orcid.org/0000-0001-6334-5186","affiliations":[{"raw_affiliation_string":"Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA 95064, United States","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064, United States","institution_ids":["https://openalex.org/I185103710"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111981457","display_name":"Russ Corbett\u2010Detig","orcid":null},"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":["Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA 95064, United States","Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomolecular Engineering, University of California Santa Cruz , Santa Cruz, CA 95064, United States","institution_ids":["https://openalex.org/I185103710"]},{"raw_affiliation_string":"Genomics Institute, University of California Santa Cruz , Santa Cruz, CA 95064, United States","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"},"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":["Electrical and Computer Engineering, University of California San Diego , La Jolla, CA 92093, United States"],"raw_orcid":"https://orcid.org/0000-0001-5600-2900","affiliations":[{"raw_affiliation_string":"Electrical and Computer Engineering, University of California San Diego , La Jolla, CA 92093, United States","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037983874","display_name":"Robert Lanfear","orcid":"https://orcid.org/0000-0002-1140-2596"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Robert Lanfear","raw_affiliation_strings":["Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2601, Australia"],"raw_orcid":"https://orcid.org/0000-0002-1140-2596","affiliations":[{"raw_affiliation_string":"Ecology and Evolution, Research School of Biology, College of Science, Australian National University , Canberra, ACT 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019880902","display_name":"B\u00f9i Quang Minh","orcid":"https://orcid.org/0000-0002-5535-6560"},"institutions":[{"id":"https://openalex.org/I118347636","display_name":"Australian National University","ror":"https://ror.org/019wvm592","country_code":"AU","type":"education","lineage":["https://openalex.org/I118347636"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Bui Quang Minh","raw_affiliation_strings":["School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2601, Australia"],"raw_orcid":"https://orcid.org/0000-0002-5535-6560","affiliations":[{"raw_affiliation_string":"School of Computing, College of Engineering and Computer Science, Australian National University , Canberra, ACT 2601, Australia","institution_ids":["https://openalex.org/I118347636"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5019880902","https://openalex.org/A5037983874"],"corresponding_institution_ids":["https://openalex.org/I118347636"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.7265,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.67073049,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"39","issue":"9","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":0.9503999948501587,"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":0.9503999948501587,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.01600000075995922,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.004399999976158142,"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/computer-science","display_name":"Computer science","score":0.7860305905342102},{"id":"https://openalex.org/keywords/header","display_name":"Header","score":0.6764066219329834},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6636280417442322},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6105278134346008},{"id":"https://openalex.org/keywords/implementation","display_name":"Implementation","score":0.6003307104110718},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5363636612892151},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.46882814168930054},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4231172204017639},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.42005306482315063},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34677132964134216},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.26807457208633423},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.1881834864616394},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.12504920363426208}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7860305905342102},{"id":"https://openalex.org/C48105269","wikidata":"https://www.wikidata.org/wiki/Q1141160","display_name":"Header","level":2,"score":0.6764066219329834},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6636280417442322},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6105278134346008},{"id":"https://openalex.org/C26713055","wikidata":"https://www.wikidata.org/wiki/Q245962","display_name":"Implementation","level":2,"score":0.6003307104110718},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5363636612892151},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.46882814168930054},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4231172204017639},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.42005306482315063},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34677132964134216},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.26807457208633423},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.1881834864616394},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.12504920363426208},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086382","descriptor_name":"COVID-19","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000086402","descriptor_name":"SARS-CoV-2","qualifier_ui":"Q000235","qualifier_name":"genetics","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015723","descriptor_name":"Gene Library","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btad536","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad536","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad536/51316859/btad536.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:37651445","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37651445","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:oai:escholarship.org:ark:/13030/qt1rd4501v","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/1rd4501v","pdf_url":"https://escholarship.org/content/qt1rd4501v/qt1rd4501v.pdf","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 39, iss 9","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:10491953","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10491953","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10491953/pdf/btad536.pdf","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/btad536","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad536","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btad536/51316859/btad536.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":[{"score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[{"id":"https://openalex.org/G1653364450","display_name":"Efficient phylogenetic methods that manage the curse of genomic complexity","funder_award_id":"DP200103151","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4386322170.pdf","grobid_xml":"https://content.openalex.org/works/W4386322170.grobid-xml"},"referenced_works_count":16,"referenced_works":["https://openalex.org/W1525734744","https://openalex.org/W1996835973","https://openalex.org/W2031611770","https://openalex.org/W2034285706","https://openalex.org/W2071465766","https://openalex.org/W2097706568","https://openalex.org/W2105329815","https://openalex.org/W2106882534","https://openalex.org/W2111647009","https://openalex.org/W2118488195","https://openalex.org/W2132926880","https://openalex.org/W2161973008","https://openalex.org/W3121953277","https://openalex.org/W3162902051","https://openalex.org/W3196426464","https://openalex.org/W6674647444"],"related_works":["https://openalex.org/W2171597999","https://openalex.org/W2189136227","https://openalex.org/W1866537546","https://openalex.org/W630850086","https://openalex.org/W3200508093","https://openalex.org/W4372053344","https://openalex.org/W3193978431","https://openalex.org/W2519240373","https://openalex.org/W2379752180","https://openalex.org/W2610007503"],"abstract_inverted_index":{"MOTIVATION:":[0],"Neighbour-Joining":[1,54,79,146],"is":[2,55,86,104,137,163],"one":[3],"of":[4,32,40,49,61,78,82,154],"the":[5,29,44,107,143],"most":[6],"widely":[7],"used":[8,175],"distance-based":[9],"phylogenetic":[10,100],"inference":[11],"methods.":[12],"However,":[13],"current":[14],"implementations":[15,60,77],"do":[16],"not":[17],"scale":[18],"well":[19],"for":[20,52,129],"datasets":[21],"with":[22,98],"more":[23],"than":[24,142],"10":[25],"000":[26,156],"sequences.":[27],"Given":[28],"increasing":[30],"pace":[31],"generating":[33,151],"new":[34,59],"sequence":[35,50],"data,":[36],"particularly":[37],"in":[38,106,176],"outbreaks":[39],"emerging":[41],"diseases,":[42],"and":[43,75,80,92,126,166,173],"already":[45],"enormous":[46],"existing":[47,62,121,145],"databases":[48],"data":[51,174],"which":[53,71],"a":[56,89,93,152],"useful":[57],"approach,":[58],"methods":[63],"are":[64,179],"warranted.":[65],"RESULTS:":[66],"Here,":[67],"we":[68],"present":[69],"DecentTree,":[70],"provides":[72],"highly":[73],"optimized":[74],"parallel":[76],"several":[81],"its":[83],"variants.":[84],"DecentTree":[85,114,136,162],"designed":[87],"as":[88],"stand-alone":[90],"application":[91],"header-only":[94],"library":[95],"easily":[96],"integrated":[97],"other":[99],"software":[101,122,147],"(e.g.":[102,148],"it":[103],"integral":[105],"popular":[108],"IQ-TREE":[109],"software).":[110],"We":[111],"show":[112],"that":[113],"shows":[115],"similar":[116],"or":[117],"improved":[118],"performance":[119],"over":[120],"(BIONJ,":[123],"Quicktree,":[124],"FastME,":[125],"RapidNJ),":[127],"especially":[128],"handling":[130],"very":[131],"large":[132],"alignments.":[133],"For":[134],"example,":[135],"up":[138],"to":[139],"6-fold":[140],"faster":[141],"fastest":[144],"RapidNJ)":[149],"when":[150],"tree":[153],"64":[155],"SARS-CoV-2":[157],"genomes.":[158],"AVAILABILITY":[159],"AND":[160],"IMPLEMENTATION:":[161],"open":[164],"source":[165],"freely":[167],"available":[168,180],"at":[169],"https://github.com/iqtree/decenttree.":[170],"All":[171],"code":[172],"this":[177],"analysis":[178],"on":[181],"Github":[182],"(https://github.com/asdcid/Comparison-of-neighbour-joining-software).":[183]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}