{"id":"https://openalex.org/W3172041485","doi":"https://doi.org/10.1093/bioinformatics/btab430","title":"MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences","display_name":"MNHN-Tree-Tools: a toolbox for tree inference using multi-scale clustering of a set of sequences","publication_year":2021,"publication_date":"2021-06-07","ids":{"openalex":"https://openalex.org/W3172041485","doi":"https://doi.org/10.1093/bioinformatics/btab430","mag":"3172041485","pmid":"https://pubmed.ncbi.nlm.nih.gov/34100911"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab430","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab430","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3947/41091832/btab430.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3947/41091832/btab430.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090454985","display_name":"Thomas Haschka","orcid":"https://orcid.org/0000-0003-1881-5489"},"institutions":[{"id":"https://openalex.org/I4210166728","display_name":"Structure et Instabilit\u00e9 des G\u00e9nomes","ror":"https://ror.org/05pchb838","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210123595","https://openalex.org/I4210128300","https://openalex.org/I4210166728"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Thomas Haschka","raw_affiliation_strings":["Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France"],"affiliations":[{"raw_affiliation_string":"Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France","institution_ids":["https://openalex.org/I4210166728"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006714263","display_name":"Lo\u0131\u0308c Ponger","orcid":"https://orcid.org/0000-0001-9222-8907"},"institutions":[{"id":"https://openalex.org/I4210166728","display_name":"Structure et Instabilit\u00e9 des G\u00e9nomes","ror":"https://ror.org/05pchb838","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210123595","https://openalex.org/I4210128300","https://openalex.org/I4210166728"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Loic Ponger","raw_affiliation_strings":["Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France"],"affiliations":[{"raw_affiliation_string":"Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France","institution_ids":["https://openalex.org/I4210166728"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053403624","display_name":"Christophe Escud\u00e9","orcid":"https://orcid.org/0000-0003-2438-5737"},"institutions":[{"id":"https://openalex.org/I4210166728","display_name":"Structure et Instabilit\u00e9 des G\u00e9nomes","ror":"https://ror.org/05pchb838","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210123595","https://openalex.org/I4210128300","https://openalex.org/I4210166728"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Christophe Escud\u00e9","raw_affiliation_strings":["Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France"],"affiliations":[{"raw_affiliation_string":"Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France","institution_ids":["https://openalex.org/I4210166728"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011027517","display_name":"Julien Mozziconacci","orcid":"https://orcid.org/0000-0001-5652-0302"},"institutions":[{"id":"https://openalex.org/I4210166728","display_name":"Structure et Instabilit\u00e9 des G\u00e9nomes","ror":"https://ror.org/05pchb838","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I154526488","https://openalex.org/I39804081","https://openalex.org/I4210123595","https://openalex.org/I4210128300","https://openalex.org/I4210166728"]},{"id":"https://openalex.org/I185839726","display_name":"Institut Universitaire de France","ror":"https://ror.org/055khg266","country_code":"FR","type":"education","lineage":["https://openalex.org/I185839726"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Julien Mozziconacci","raw_affiliation_strings":["Institut Universitaire de 1 , rue Descartes 75005 Paris, France","Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France"],"affiliations":[{"raw_affiliation_string":"Institut Universitaire de 1 , rue Descartes 75005 Paris, France","institution_ids":["https://openalex.org/I185839726"]},{"raw_affiliation_string":"Mus\u00e9um National d\u2019Histoire Naturelle, Structure et Instabilit\u00e9 des G\u00e9nomes, UMR7196 , Paris 75231, France","institution_ids":["https://openalex.org/I4210166728"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5011027517","https://openalex.org/A5090454985"],"corresponding_institution_ids":["https://openalex.org/I185839726","https://openalex.org/I4210166728"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.1609,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.48007479,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"37","issue":"21","first_page":"3947","last_page":"3949"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":1.0,"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":1.0,"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":0.9979000091552734,"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/T12640","display_name":"Environmental DNA in Biodiversity Studies","score":0.9926999807357788,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6901088953018188},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6544378399848938},{"id":"https://openalex.org/keywords/toolbox","display_name":"Toolbox","score":0.6287115216255188},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.48990434408187866},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4748701751232147},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.43542391061782837},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3897912800312042},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3382461667060852},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3376082181930542},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.20124953985214233},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.17467862367630005},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11932384967803955}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6901088953018188},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6544378399848938},{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.6287115216255188},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.48990434408187866},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4748701751232147},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.43542391061782837},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3897912800312042},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3382461667060852},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3376082181930542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.20124953985214233},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.17467862367630005},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11932384967803955},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","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":"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":"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":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btab430","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab430","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3947/41091832/btab430.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34100911","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34100911","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:HAL:hal-03451406v1","is_oa":true,"landing_page_url":"https://hal.science/hal-03451406","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2021, &#x27E8;10.1093/bioinformatics/btab430&#x27E9;","raw_type":"Journal articles"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btab430","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab430","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/37/21/3947/41091832/btab430.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.5,"id":"https://metadata.un.org/sdg/12"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324506","display_name":"Mus\u00e9um National d'Histoire Naturelle","ror":"https://ror.org/03wkt5x30"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3172041485.pdf","grobid_xml":"https://content.openalex.org/works/W3172041485.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1984222112","https://openalex.org/W1990966781","https://openalex.org/W2019952619","https://openalex.org/W2029195137","https://openalex.org/W2087064593","https://openalex.org/W2103692338","https://openalex.org/W2119531100","https://openalex.org/W2154026962","https://openalex.org/W2160642098","https://openalex.org/W2194764270","https://openalex.org/W2396849069","https://openalex.org/W2513506562","https://openalex.org/W2952626329","https://openalex.org/W2966700757"],"related_works":["https://openalex.org/W4205140848","https://openalex.org/W2068663075","https://openalex.org/W2978678743","https://openalex.org/W2797837731","https://openalex.org/W4393677513","https://openalex.org/W4390832911","https://openalex.org/W829257147","https://openalex.org/W4385302116","https://openalex.org/W2150344375","https://openalex.org/W1970242467"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
