{"id":"https://openalex.org/W2130208436","doi":"https://doi.org/10.1093/bib/bbr009","title":"A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis","display_name":"A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis","publication_year":2011,"publication_date":"2011-04-27","ids":{"openalex":"https://openalex.org/W2130208436","doi":"https://doi.org/10.1093/bib/bbr009","mag":"2130208436","pmid":"https://pubmed.ncbi.nlm.nih.gov/21525143"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbr009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr009","pdf_url":"https://academic.oup.com/bib/article-pdf/13/1/107/581529/bbr009.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/13/1/107/581529/bbr009.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039662308","display_name":"Yijun Sun","orcid":"https://orcid.org/0000-0003-0610-6132"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Y. Sun","raw_affiliation_strings":["Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA. sunyijun@biotech.ufl.edu","Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA. sunyijun@biotech.ufl.edu","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090194899","display_name":"Yunpeng Cai","orcid":"https://orcid.org/0000-0001-8797-4243"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Y. Cai","raw_affiliation_strings":["Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","University of Florida","Department of Chemistry and Biochemistry, University of Colorado at Boulder","Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Colorado at Boulder","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108431980","display_name":"S. M. Huse","orcid":null},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. M. Huse","raw_affiliation_strings":["Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","Department of Chemistry and Biochemistry, University of Colorado at Boulder","Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","University of Florida"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Colorado at Boulder","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","institution_ids":[]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033881627","display_name":"Rob Knight","orcid":"https://orcid.org/0000-0002-0975-9019"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]},{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"R. Knight","raw_affiliation_strings":["University of Florida","Department of Chemistry and Biochemistry, University of Colorado at Boulder","Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA"],"affiliations":[{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Colorado at Boulder","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","institution_ids":[]},{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084450417","display_name":"William G. Farmerie","orcid":"https://orcid.org/0000-0002-1627-8774"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"W. G. Farmerie","raw_affiliation_strings":["Department of Chemistry and Biochemistry, University of Colorado at Boulder","Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","University of Florida","Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA"],"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Colorado at Boulder","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","institution_ids":[]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051929404","display_name":"X. Wang","orcid":"https://orcid.org/0000-0002-8034-5628"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"X. Wang","raw_affiliation_strings":["Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","University of Florida","Department of Chemistry and Biochemistry, University of Colorado at Boulder","Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Colorado at Boulder","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5048359764","display_name":"Volker Mai","orcid":"https://orcid.org/0000-0002-6997-9750"},"institutions":[{"id":"https://openalex.org/I188538660","display_name":"University of Colorado Boulder","ror":"https://ror.org/02ttsq026","country_code":"US","type":"education","lineage":["https://openalex.org/I188538660"]},{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"V. Mai","raw_affiliation_strings":["Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","Department of Chemistry and Biochemistry, University of Colorado at Boulder","University of Florida","Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Center for Biotechnology Research, University of Florida, PO Box 103622, Gainesville, FL 32610-3622, USA","institution_ids":[]},{"raw_affiliation_string":"Department of Chemistry and Biochemistry, University of Colorado at Boulder","institution_ids":["https://openalex.org/I188538660"]},{"raw_affiliation_string":"University of Florida","institution_ids":["https://openalex.org/I33213144"]},{"raw_affiliation_string":"Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5039662308"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":7.8172,"has_fulltext":true,"cited_by_count":167,"citation_normalized_percentile":{"value":0.98302406,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"13","issue":"1","first_page":"107","last_page":"121"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10066","display_name":"Gut microbiota and health","score":0.9995999932289124,"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/T10066","display_name":"Gut microbiota and health","score":0.9995999932289124,"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/T11791","display_name":"Microbial Community Ecology and Physiology","score":0.9965000152587891,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9954000115394592,"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/benchmark","display_name":"Benchmark (surveying)","score":0.8050506114959717},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.7876185178756714},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7775766849517822},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.6040504574775696},{"id":"https://openalex.org/keywords/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.48016634583473206},{"id":"https://openalex.org/keywords/scale","display_name":"Scale (ratio)","score":0.4350448548793793},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.410499632358551},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.349919855594635},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3208227753639221}],"concepts":[{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.8050506114959717},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.7876185178756714},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7775766849517822},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.6040504574775696},{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.48016634583473206},{"id":"https://openalex.org/C2778755073","wikidata":"https://www.wikidata.org/wiki/Q10858537","display_name":"Scale (ratio)","level":2,"score":0.4350448548793793},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.410499632358551},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.349919855594635},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3208227753639221},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012336","descriptor_name":"RNA, Ribosomal, 16S","qualifier_ui":"Q000235","qualifier_name":"genetics","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":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"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":"D058448","descriptor_name":"Biota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058448","descriptor_name":"Biota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058448","descriptor_name":"Biota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbr009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr009","pdf_url":"https://academic.oup.com/bib/article-pdf/13/1/107/581529/bbr009.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21525143","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21525143","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:europepmc.org:2530430","is_oa":false,"landing_page_url":"http://europepmc.org/articles/PMC3251834","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3251834","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3251834","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbr009","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbr009","pdf_url":"https://academic.oup.com/bib/article-pdf/13/1/107/581529/bbr009.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.4399999976158142}],"awards":[],"funders":[{"id":"https://openalex.org/F4320306151","display_name":"Alfred P. Sloan Foundation","ror":"https://ror.org/052csg198"},{"id":"https://openalex.org/F4320306159","display_name":"W. M. Keck Foundation","ror":"https://ror.org/000dswa46"},{"id":"https://openalex.org/F4320309652","display_name":"University of Michigan","ror":"https://ror.org/00jmfr291"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2130208436.pdf","grobid_xml":"https://content.openalex.org/works/W2130208436.grobid-xml"},"referenced_works_count":36,"referenced_works":["https://openalex.org/W1987184081","https://openalex.org/W2000072710","https://openalex.org/W2016381774","https://openalex.org/W2021380741","https://openalex.org/W2030154486","https://openalex.org/W2055043387","https://openalex.org/W2059237622","https://openalex.org/W2067474031","https://openalex.org/W2072970694","https://openalex.org/W2073378124","https://openalex.org/W2073548709","https://openalex.org/W2084793748","https://openalex.org/W2087671769","https://openalex.org/W2093996595","https://openalex.org/W2097875133","https://openalex.org/W2099117570","https://openalex.org/W2102502076","https://openalex.org/W2103805072","https://openalex.org/W2105456967","https://openalex.org/W2108211735","https://openalex.org/W2108718991","https://openalex.org/W2118001436","https://openalex.org/W2124351063","https://openalex.org/W2131186249","https://openalex.org/W2132598047","https://openalex.org/W2132926880","https://openalex.org/W2135365149","https://openalex.org/W2140638310","https://openalex.org/W2149573313","https://openalex.org/W2150914285","https://openalex.org/W2155066423","https://openalex.org/W2162315106","https://openalex.org/W2171571559","https://openalex.org/W2171901261","https://openalex.org/W4236236547","https://openalex.org/W4245436919"],"related_works":["https://openalex.org/W2592952084","https://openalex.org/W3216028647","https://openalex.org/W4386246753","https://openalex.org/W2032933424","https://openalex.org/W4229003453","https://openalex.org/W2020701082","https://openalex.org/W3197105638","https://openalex.org/W188786151","https://openalex.org/W3192757256","https://openalex.org/W2165213086"],"abstract_inverted_index":{"Recent":[0],"advances":[1],"in":[2,30,40,64,116,131,136,164],"massively":[3],"parallel":[4],"sequencing":[5],"technology":[6],"have":[7,37],"created":[8],"new":[9,76],"opportunities":[10],"to":[11,85,97],"probe":[12],"the":[13,21,27,41,89,103,151,160],"hidden":[14],"world":[15],"of":[16,20,35,73,102,106,123,134,150,159,166],"microbes.":[17],"Taxonomy-independent":[18],"clustering":[19,104,155,170],"16S":[22],"rRNA":[23],"gene":[24],"is":[25,49],"usually":[26],"first":[28],"step":[29],"analyzing":[31],"microbial":[32],"communities.":[33],"Dozens":[34],"algorithms":[36,54,84,162],"been":[38],"developed":[39,80,145],"last":[42],"decade,":[43],"but":[44],"a":[45,65,99,147],"comprehensive":[46],"benchmark":[47,67,140],"study":[48,68,141],"lacking.":[50],"Here,":[51],"we":[52],"survey":[53],"currently":[55],"used":[56],"by":[57],"microbiologists,":[58],"and":[59,92,119,169],"compare":[60],"seven":[61],"representative":[62],"methods":[63,113],"large-scale":[66],"that":[69,81,111,120],"addresses":[70],"several":[71,93],"issues":[72],"concern.":[74],"A":[75],"experimental":[77],"protocol":[78],"was":[79],"allows":[82],"different":[83],"be":[86],"compared":[87],"using":[88],"same":[90],"platform,":[91],"criteria":[94],"were":[95],"introduced":[96],"facilitate":[98],"quantitative":[100],"evaluation":[101],"performance":[105],"each":[107],"algorithm.":[108],"We":[109],"found":[110],"existing":[112],"vary":[114],"widely":[115],"their":[117],"outputs,":[118],"inappropriate":[121],"use":[122],"distance":[124],"levels":[125],"for":[126],"taxonomic":[127],"assignments":[128],"likely":[129],"resulted":[130],"substantial":[132],"overestimates":[133],"biodiversity":[135],"many":[137],"studies.":[138],"The":[139],"identified":[142],"our":[143],"recently":[144],"ESPRIT-Tree,":[146],"fast":[148],"implementation":[149],"average":[152],"linkage-based":[153],"hierarchical":[154],"algorithm,":[156],"as":[157],"one":[158],"best":[161],"available":[163],"terms":[165],"computational":[167],"efficiency":[168],"accuracy.":[171]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":9},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":14},{"year":2016,"cited_by_count":19},{"year":2015,"cited_by_count":21},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":25},{"year":2012,"cited_by_count":16}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}