{"id":"https://openalex.org/W2111802622","doi":"https://doi.org/10.1093/bioinformatics/btl478","title":"Clearcut: a fast implementation of relaxed neighbor joining","display_name":"Clearcut: a fast implementation of relaxed neighbor joining","publication_year":2006,"publication_date":"2006-09-18","ids":{"openalex":"https://openalex.org/W2111802622","doi":"https://doi.org/10.1093/bioinformatics/btl478","mag":"2111802622","pmid":"https://pubmed.ncbi.nlm.nih.gov/16982706"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl478","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl478","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5052350543","display_name":"Luke Sheneman","orcid":"https://orcid.org/0000-0001-8781-2041"},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Luke Sheneman","raw_affiliation_strings":["Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA","Department of Biological Sciences, University of Idaho, Moscow, ID, USA;"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho, Moscow, ID, USA;","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101058238","display_name":"Jason Evans","orcid":null},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jason Evans","raw_affiliation_strings":["Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA","Department of Biological Sciences, University of Idaho, Moscow, ID, USA;"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho, Moscow, ID, USA;","institution_ids":["https://openalex.org/I155093810"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061637086","display_name":"James A. Foster","orcid":"https://orcid.org/0000-0002-6770-6521"},"institutions":[{"id":"https://openalex.org/I155093810","display_name":"University of Idaho","ror":"https://ror.org/03hbp5t65","country_code":"US","type":"education","lineage":["https://openalex.org/I155093810"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James A. Foster","raw_affiliation_strings":["Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA","Department of Biological Sciences, University of Idaho, Moscow, ID, USA;"],"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho \u00a0 Moscow, ID, USA","institution_ids":["https://openalex.org/I155093810"]},{"raw_affiliation_string":"Department of Biological Sciences, University of Idaho, Moscow, ID, USA;","institution_ids":["https://openalex.org/I155093810"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5052350543"],"corresponding_institution_ids":["https://openalex.org/I155093810"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.1793,"has_fulltext":false,"cited_by_count":187,"citation_normalized_percentile":{"value":0.86827127,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"22","issue":"22","first_page":"2823","last_page":"2824"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9797000288963318,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9700000286102295,"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/pairwise-comparison","display_name":"Pairwise comparison","score":0.7376000881195068},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.715340256690979},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.7106292843818665},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5896902680397034},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5466802716255188},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5435393452644348},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.49511972069740295},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.48734697699546814},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.4518269896507263},{"id":"https://openalex.org/keywords/matrix","display_name":"Matrix (chemical analysis)","score":0.4449804425239563},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.42236828804016113},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3383646607398987},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.253741055727005},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2517051696777344},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15584135055541992},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08620226383209229}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7376000881195068},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.715340256690979},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.7106292843818665},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5896902680397034},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5466802716255188},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5435393452644348},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.49511972069740295},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.48734697699546814},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.4518269896507263},{"id":"https://openalex.org/C106487976","wikidata":"https://www.wikidata.org/wiki/Q685816","display_name":"Matrix (chemical analysis)","level":2,"score":0.4449804425239563},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.42236828804016113},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3383646607398987},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.253741055727005},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2517051696777344},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15584135055541992},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08620226383209229},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"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":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btl478","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl478","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16982706","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16982706","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:CiteSeerX.psu:10.1.1.101.506","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.101.506","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btl478v1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W241117969","https://openalex.org/W1525734744","https://openalex.org/W1600348603","https://openalex.org/W1814244002","https://openalex.org/W1973912434","https://openalex.org/W2065461553","https://openalex.org/W2097706568","https://openalex.org/W2107594154","https://openalex.org/W2109586018","https://openalex.org/W2118488195","https://openalex.org/W2119831725","https://openalex.org/W3199943451","https://openalex.org/W6609214399","https://openalex.org/W6638395436","https://openalex.org/W6674647444","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2114617541","https://openalex.org/W2362218761","https://openalex.org/W2062354928","https://openalex.org/W2113708670","https://openalex.org/W2088120817","https://openalex.org/W1649917817","https://openalex.org/W240043582"],"abstract_inverted_index":{"Clearcut":[0],"source":[1],"code":[2],"is":[3],"available":[4],"for":[5],"download":[6],"at:":[7],"http://bioinformatics.hungry.com/clearcut":[8]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":14},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":10},{"year":2018,"cited_by_count":17},{"year":2017,"cited_by_count":18},{"year":2016,"cited_by_count":12},{"year":2015,"cited_by_count":11},{"year":2014,"cited_by_count":13},{"year":2013,"cited_by_count":14},{"year":2012,"cited_by_count":13}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}