{"id":"https://openalex.org/W2157701114","doi":"https://doi.org/10.1093/bioinformatics/btq243","title":"The Newick utilities: high-throughput phylogenetic tree processing in the U<scp>nix</scp> shell","display_name":"The Newick utilities: high-throughput phylogenetic tree processing in the U<scp>nix</scp> shell","publication_year":2010,"publication_date":"2010-05-13","ids":{"openalex":"https://openalex.org/W2157701114","doi":"https://doi.org/10.1093/bioinformatics/btq243","mag":"2157701114","pmid":"https://pubmed.ncbi.nlm.nih.gov/20472542"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/13/1669/48852067/bioinformatics_26_13_1669.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/26/13/1669/48852067/bioinformatics_26_13_1669.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040004109","display_name":"Thomas Junier","orcid":"https://orcid.org/0000-0002-4015-5969"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]},{"id":"https://openalex.org/I114457229","display_name":"University of Geneva","ror":"https://ror.org/01swzsf04","country_code":"CH","type":"education","lineage":["https://openalex.org/I114457229"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","GB"],"is_corresponding":true,"raw_author_name":"Thomas Junier","raw_affiliation_strings":["1 Department of Genetic Medicine and Development, University of Geneva Medical School, 2 Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 3 Imperial College London, South Kensington Campus, SW7 2AZ, London, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetic Medicine and Development, University of Geneva Medical School, 2 Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 3 Imperial College London, South Kensington Campus, SW7 2AZ, London, UK","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I114457229","https://openalex.org/I47508984"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029893038","display_name":"Evgeny M. Zdobnov","orcid":"https://orcid.org/0000-0002-5178-1498"},"institutions":[{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]},{"id":"https://openalex.org/I114457229","display_name":"University of Geneva","ror":"https://ror.org/01swzsf04","country_code":"CH","type":"education","lineage":["https://openalex.org/I114457229"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH","GB"],"is_corresponding":false,"raw_author_name":"Evgeny M. Zdobnov","raw_affiliation_strings":["1 Department of Genetic Medicine and Development, University of Geneva Medical School, 2 Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 3 Imperial College London, South Kensington Campus, SW7 2AZ, London, UK"],"affiliations":[{"raw_affiliation_string":"1 Department of Genetic Medicine and Development, University of Geneva Medical School, 2 Swiss Institute of Bioinformatics, 1 rue Michel-Servet, 1211 Geneva, Switzerland and 3 Imperial College London, South Kensington Campus, SW7 2AZ, London, UK","institution_ids":["https://openalex.org/I12708293","https://openalex.org/I114457229","https://openalex.org/I47508984"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5040004109"],"corresponding_institution_ids":["https://openalex.org/I114457229","https://openalex.org/I12708293","https://openalex.org/I47508984"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":2.8464,"has_fulltext":false,"cited_by_count":811,"citation_normalized_percentile":{"value":0.91054327,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"26","issue":"13","first_page":"1669","last_page":"1670"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9900000095367432,"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/T10487","display_name":"Plant and animal studies","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.7958023548126221},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7742271423339844},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7734228372573853},{"id":"https://openalex.org/keywords/scalable-vector-graphics","display_name":"Scalable Vector Graphics","score":0.6497511863708496},{"id":"https://openalex.org/keywords/ascii","display_name":"ASCII","score":0.6495820879936218},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5811487436294556},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.5279288291931152},{"id":"https://openalex.org/keywords/unix","display_name":"Unix","score":0.5212467312812805},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.4834212064743042},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.4790421724319458},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.42038577795028687},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.4171525239944458},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.29194867610931396},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18662312626838684}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.7958023548126221},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7742271423339844},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7734228372573853},{"id":"https://openalex.org/C202629362","wikidata":"https://www.wikidata.org/wiki/Q2078","display_name":"Scalable Vector Graphics","level":2,"score":0.6497511863708496},{"id":"https://openalex.org/C196832560","wikidata":"https://www.wikidata.org/wiki/Q8815","display_name":"ASCII","level":2,"score":0.6495820879936218},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5811487436294556},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.5279288291931152},{"id":"https://openalex.org/C112968700","wikidata":"https://www.wikidata.org/wiki/Q11368","display_name":"Unix","level":3,"score":0.5212467312812805},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.4834212064743042},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.4790421724319458},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.42038577795028687},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.4171525239944458},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.29194867610931396},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18662312626838684},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":"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":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","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":"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":5,"locations":[{"id":"doi:10.1093/bioinformatics/btq243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/13/1669/48852067/bioinformatics_26_13_1669.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:20472542","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20472542","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:doc.rero.ch:304329","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:pubmedcentral.nih.gov:2887050","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2887050","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:unige.ch:aou:unige:21032","is_oa":true,"landing_page_url":"https://archive-ouverte.unige.ch/unige:21032","pdf_url":null,"source":{"id":"https://openalex.org/S4306402259","display_name":"Archive ouverte UNIGE (University of Geneva)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I114457229","host_organization_name":"University of Geneva","host_organization_lineage":["https://openalex.org/I114457229"],"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":"ISSN: 1367-4803","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btq243","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq243","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/26/13/1669/48852067/bioinformatics_26_13_1669.pdf","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8333493075","display_name":"Computational comparative analysis of insect genomes","funder_award_id":"112588","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G8832621192","display_name":null,"funder_award_id":"3100A0","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2157701114.pdf","grobid_xml":"https://content.openalex.org/works/W2157701114.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1494031014","https://openalex.org/W1990096140","https://openalex.org/W1993038297","https://openalex.org/W1996423252","https://openalex.org/W2102546693","https://openalex.org/W2103546861","https://openalex.org/W2124967403","https://openalex.org/W2132926880","https://openalex.org/W2150934173","https://openalex.org/W2151409320","https://openalex.org/W2582743722","https://openalex.org/W3199943451","https://openalex.org/W6629740270","https://openalex.org/W6800717233"],"related_works":["https://openalex.org/W2358969090","https://openalex.org/W3183425535","https://openalex.org/W2354624479","https://openalex.org/W2394137533","https://openalex.org/W2362190996","https://openalex.org/W629813691","https://openalex.org/W2385461408","https://openalex.org/W2119089902","https://openalex.org/W2387643967","https://openalex.org/W2393464257"],"abstract_inverted_index":{"thomas.junier@unige.ch":[0]},"counts_by_year":[{"year":2026,"cited_by_count":23},{"year":2025,"cited_by_count":137},{"year":2024,"cited_by_count":109},{"year":2023,"cited_by_count":102},{"year":2022,"cited_by_count":90},{"year":2021,"cited_by_count":113},{"year":2020,"cited_by_count":61},{"year":2019,"cited_by_count":40},{"year":2018,"cited_by_count":30},{"year":2017,"cited_by_count":20},{"year":2016,"cited_by_count":17},{"year":2015,"cited_by_count":29},{"year":2014,"cited_by_count":19},{"year":2013,"cited_by_count":11},{"year":2012,"cited_by_count":6}],"updated_date":"2026-04-24T08:23:43.765630","created_date":"2016-06-24T00:00:00"}
