{"id":"https://openalex.org/W7155400604","doi":"https://doi.org/10.1093/bioinformatics/btag195","title":"treestructure: an R package to detect population structure in phylogenetic trees","display_name":"treestructure: an R package to detect population structure in phylogenetic trees","publication_year":2026,"publication_date":"2026-04-20","ids":{"openalex":"https://openalex.org/W7155400604","doi":"https://doi.org/10.1093/bioinformatics/btag195","pmid":"https://pubmed.ncbi.nlm.nih.gov/42024618"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btag195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag195","pdf_url":null,"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://doi.org/10.1093/bioinformatics/btag195","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5134407858","display_name":"Fabr\u00edcia F Nascimento","orcid":null},"institutions":[{"id":"https://openalex.org/I4210163563","display_name":"London Centre for Neglected Tropical Disease Research","ror":"https://ror.org/05jx29z89","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210163563"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Fabr\u00edcia F Nascimento","raw_affiliation_strings":["MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,"],"raw_orcid":"https://orcid.org/0000-0001-9426-6835","affiliations":[{"raw_affiliation_string":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,","institution_ids":["https://openalex.org/I4210163563"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032802516","display_name":"Vin\u00edcius Bonetti Franceschi","orcid":"https://orcid.org/0000-0002-0006-9337"},"institutions":[{"id":"https://openalex.org/I4210163563","display_name":"London Centre for Neglected Tropical Disease Research","ror":"https://ror.org/05jx29z89","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210163563"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Vinicius B Franceschi","raw_affiliation_strings":["MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,"],"raw_orcid":"https://orcid.org/0000-0002-0006-9337","affiliations":[{"raw_affiliation_string":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,","institution_ids":["https://openalex.org/I4210163563"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5058253520","display_name":"Erik Volz","orcid":"https://orcid.org/0000-0001-6268-8937"},"institutions":[{"id":"https://openalex.org/I4210163563","display_name":"London Centre for Neglected Tropical Disease Research","ror":"https://ror.org/05jx29z89","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210163563"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Erik M Volz","raw_affiliation_strings":["MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,"],"raw_orcid":"https://orcid.org/0000-0001-6268-8937","affiliations":[{"raw_affiliation_string":"MRC Centre for Global Infectious Disease Analysis, Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London , London, W12 0BZ,","institution_ids":["https://openalex.org/I4210163563"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5058253520"],"corresponding_institution_ids":["https://openalex.org/I4210163563"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.56427817,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"42","issue":"5","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.6485999822616577,"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"}},"topics":[{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.6485999822616577,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.1216999962925911,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.10949999839067459,"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/coalescent-theory","display_name":"Coalescent theory","score":0.8323000073432922},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7321000099182129},{"id":"https://openalex.org/keywords/population","display_name":"Population","score":0.6711000204086304},{"id":"https://openalex.org/keywords/population-structure","display_name":"Population structure","score":0.6011999845504761},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.5271000266075134},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.44909998774528503},{"id":"https://openalex.org/keywords/statistical-model","display_name":"Statistical model","score":0.3249000012874603},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.32089999318122864}],"concepts":[{"id":"https://openalex.org/C2554327","wikidata":"https://www.wikidata.org/wiki/Q2698599","display_name":"Coalescent theory","level":4,"score":0.8323000073432922},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7321000099182129},{"id":"https://openalex.org/C2908647359","wikidata":"https://www.wikidata.org/wiki/Q2625603","display_name":"Population","level":2,"score":0.6711000204086304},{"id":"https://openalex.org/C2983611323","wikidata":"https://www.wikidata.org/wiki/Q7229822","display_name":"Population structure","level":3,"score":0.6011999845504761},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.5271000266075134},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4708999991416931},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.44909998774528503},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.43709999322891235},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34450000524520874},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32910001277923584},{"id":"https://openalex.org/C114289077","wikidata":"https://www.wikidata.org/wiki/Q3284399","display_name":"Statistical model","level":2,"score":0.3249000012874603},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32249999046325684},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.32089999318122864},{"id":"https://openalex.org/C85721925","wikidata":"https://www.wikidata.org/wiki/Q31151","display_name":"Population genetics","level":3,"score":0.31380000710487366},{"id":"https://openalex.org/C81977670","wikidata":"https://www.wikidata.org/wiki/Q585259","display_name":"Genetic diversity","level":3,"score":0.30720001459121704},{"id":"https://openalex.org/C52079815","wikidata":"https://www.wikidata.org/wiki/Q7229808","display_name":"Population model","level":3,"score":0.303600013256073},{"id":"https://openalex.org/C93518851","wikidata":"https://www.wikidata.org/wiki/Q180160","display_name":"Metadata","level":2,"score":0.29750001430511475},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.28940001130104065},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.2892000079154968},{"id":"https://openalex.org/C2781316041","wikidata":"https://www.wikidata.org/wiki/Q1230584","display_name":"Diversity (politics)","level":2,"score":0.2865999937057495},{"id":"https://openalex.org/C98722961","wikidata":"https://www.wikidata.org/wiki/Q7189436","display_name":"Phylogenetic diversity","level":4,"score":0.28060001134872437},{"id":"https://openalex.org/C46576788","wikidata":"https://www.wikidata.org/wiki/Q5532925","display_name":"Genetic structure","level":4,"score":0.27149999141693115},{"id":"https://openalex.org/C197583594","wikidata":"https://www.wikidata.org/wiki/Q1052390","display_name":"Most recent common ancestor","level":4,"score":0.26579999923706055},{"id":"https://openalex.org/C49781872","wikidata":"https://www.wikidata.org/wiki/Q1045555","display_name":"Maximum likelihood","level":2,"score":0.2648000121116638},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.25589999556541443}],"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":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D005828","descriptor_name":"Genetics, Population","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btag195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag195","pdf_url":null,"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:42024618","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/42024618","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:pubmedcentral.nih.gov:13171169","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC13171169/","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":"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/btag195","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btag195","pdf_url":null,"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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":10,"referenced_works":["https://openalex.org/W2085487226","https://openalex.org/W2516104505","https://openalex.org/W2950753995","https://openalex.org/W3005546911","https://openalex.org/W3099697243","https://openalex.org/W4206338751","https://openalex.org/W4225522864","https://openalex.org/W4402331895","https://openalex.org/W4411721550","https://openalex.org/W4412612303"],"related_works":[],"abstract_inverted_index":{"MOTIVATION:":[0],"How":[1],"population":[2,13,36,48,77],"structure":[3,37,49,78],"can":[4,23],"shape":[5],"genetic":[6],"diversity":[7],"is":[8,31,50,86],"a":[9,67,80],"longstanding":[10],"problem":[11],"in":[12,79],"genetics.":[14],"While":[15],"the":[16,46],"use":[17],"of":[18,27,60],"geographic":[19],"locations,":[20],"when":[21,38,45],"available,":[22],"help":[24],"answer":[25],"some":[26],"these":[28],"questions,":[29],"it":[30],"still":[32],"difficult":[33],"to":[34,74],"determine":[35],"such":[39],"metadata":[40],"are":[41],"not":[42,51],"available":[43,87],"or":[44],"potential":[47],"easily":[52],"observed.":[53],"Here,":[54],"we":[55],"present":[56],"an":[57,62],"updated":[58],"version":[59],"treestructure,":[61],"R":[63],"package":[64],"that":[65],"implements":[66],"statistical":[68],"test":[69],"based":[70],"on":[71],"coalescent":[72],"theory":[73],"detect":[75],"unobserved":[76],"time-scaled":[81],"phylogenetic":[82],"tree.":[83],"AVAILABILITY:":[84],"treestructure":[85],"at":[88,90,93],"CRAN":[89],"https://cloud.r-project.org/web/packages/treestructure/":[91],"and":[92],"https://emvolz-phylodynamics.github.io/treestructure/.":[94]},"counts_by_year":[],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2026-04-24T00:00:00"}
