{"id":"https://openalex.org/W2883251903","doi":"https://doi.org/10.1093/bioinformatics/bty633","title":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","display_name":"ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R","publication_year":2018,"publication_date":"2018-07-14","ids":{"openalex":"https://openalex.org/W2883251903","doi":"https://doi.org/10.1093/bioinformatics/bty633","mag":"2883251903","pmid":"https://pubmed.ncbi.nlm.nih.gov/30016406"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty633","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty633","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/526/27699799/bty633.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/35/3/526/27699799/bty633.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091069787","display_name":"Emmanuel Paradis","orcid":"https://orcid.org/0000-0003-3092-2199"},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I159885104","display_name":"\u00c9cole Pratique des Hautes \u00c9tudes","ror":"https://ror.org/046b3cj80","country_code":"FR","type":"education","lineage":["https://openalex.org/I159885104","https://openalex.org/I2746051580"]},{"id":"https://openalex.org/I19894307","display_name":"Universit\u00e9 de Montpellier","ror":"https://ror.org/051escj72","country_code":"FR","type":"education","lineage":["https://openalex.org/I19894307"]},{"id":"https://openalex.org/I4210105943","display_name":"Institut des Sciences de l'Evolution de Montpellier","ror":"https://ror.org/01cah1n37","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I131077856","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I2746051580","https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210105943","https://openalex.org/I4210107625","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]},{"id":"https://openalex.org/I4210166444","display_name":"Institut de Recherche pour le D\u00e9veloppement","ror":"https://ror.org/05q3vnk25","country_code":"FR","type":"government","lineage":["https://openalex.org/I2802818602","https://openalex.org/I4210090127","https://openalex.org/I4210131494","https://openalex.org/I4210166444"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Emmanuel Paradis","raw_affiliation_strings":["ISEM, IRD, Univ. Montpellier, CNRS, EPHE, Montpellier, France"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ISEM, IRD, Univ. Montpellier, CNRS, EPHE, Montpellier, France","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I4210105943","https://openalex.org/I4210166444"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034075696","display_name":"Klaus Schliep","orcid":"https://orcid.org/0000-0003-2941-0161"},"institutions":[{"id":"https://openalex.org/I33434090","display_name":"University of Massachusetts Boston","ror":"https://ror.org/04ydmy275","country_code":"US","type":"education","lineage":["https://openalex.org/I33434090"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Klaus Schliep","raw_affiliation_strings":["Department of Biology, University of Massachusetts Boston, Boston, MA, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Massachusetts Boston, Boston, MA, USA","institution_ids":["https://openalex.org/I33434090"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5091069787"],"corresponding_institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I159885104","https://openalex.org/I19894307","https://openalex.org/I4210105943","https://openalex.org/I4210166444"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":521.9814,"has_fulltext":true,"cited_by_count":9828,"citation_normalized_percentile":{"value":0.99998862,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"35","issue":"3","first_page":"526","last_page":"528"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13398","display_name":"Data Analysis with R","score":0.25870001316070557,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13398","display_name":"Data Analysis with R","score":0.25870001316070557,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10895","display_name":"Species Distribution and Climate Change","score":0.19169999659061432,"subfield":{"id":"https://openalex.org/subfields/2302","display_name":"Ecological Modeling"},"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/T10699","display_name":"Primate Behavior and Ecology","score":0.06509999930858612,"subfield":{"id":"https://openalex.org/subfields/3207","display_name":"Social Psychology"},"field":{"id":"https://openalex.org/fields/32","display_name":"Psychology"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/flexibility","display_name":"Flexibility (engineering)","score":0.7155007123947144},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.7020860314369202},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.6858317255973816},{"id":"https://openalex.org/keywords/software-package","display_name":"Software package","score":0.6359310150146484},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5524345636367798},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5419744849205017},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4705904722213745},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.41612082719802856},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4132831394672394},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3018162250518799},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.24455484747886658},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09801638126373291},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08200851082801819},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.07850086688995361}],"concepts":[{"id":"https://openalex.org/C2780598303","wikidata":"https://www.wikidata.org/wiki/Q65921492","display_name":"Flexibility (engineering)","level":2,"score":0.7155007123947144},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.7020860314369202},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.6858317255973816},{"id":"https://openalex.org/C3020440742","wikidata":"https://www.wikidata.org/wiki/Q1176855","display_name":"Software package","level":3,"score":0.6359310150146484},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5524345636367798},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5419744849205017},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4705904722213745},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.41612082719802856},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4132831394672394},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3018162250518799},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.24455484747886658},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09801638126373291},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08200851082801819},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.07850086688995361},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":"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":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D044822","descriptor_name":"Biodiversity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bty633","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty633","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/526/27699799/bty633.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:30016406","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30016406","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":"Journal Article"},{"id":"pmh:oai:HAL:ird-01920132v1","is_oa":false,"landing_page_url":"https://ird.hal.science/ird-01920132","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2019, 35 (3), pp.526-528. &#x27E8;10.1093/bioinformatics/bty633&#x27E9;","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty633","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty633","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/35/3/526/27699799/bty633.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":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2883251903.pdf","grobid_xml":"https://content.openalex.org/works/W2883251903.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W585085135","https://openalex.org/W1973094248","https://openalex.org/W2097734528","https://openalex.org/W2151409320","https://openalex.org/W2582743722","https://openalex.org/W3006062678","https://openalex.org/W3026575013","https://openalex.org/W3031157003","https://openalex.org/W3033513140","https://openalex.org/W3082589942"],"related_works":["https://openalex.org/W3082463427","https://openalex.org/W2566205467","https://openalex.org/W4254478096","https://openalex.org/W1855874432","https://openalex.org/W1985266044","https://openalex.org/W1584884842","https://openalex.org/W2108252494","https://openalex.org/W1970802890","https://openalex.org/W2157390150","https://openalex.org/W2037418048"],"abstract_inverted_index":{"Summary:":[0],"After":[1],"more":[2],"than":[3],"fifteen":[4],"years":[5],"of":[6,25,29,59,80,87],"existence,":[7],"the":[8,78,98],"R":[9,100],"package":[10],"ape":[11,73,94],"has":[12,18,32],"continuously":[13],"grown":[14],"its":[15],"contents,":[16],"and":[17,61,82,92],"been":[19,45],"used":[20],"by":[21],"a":[22,34,37,65,74,85],"growing":[23],"community":[24],"users.":[26],"The":[27],"release":[28],"version":[30],"5.0":[31],"marked":[33],"leap":[35],"towards":[36],"modern":[38],"software":[39,76],"for":[40,52,77],"evolutionary":[41],"analyses.":[42],"Efforts":[43],"have":[44],"put":[46],"to":[47],"improve":[48],"efficiency,":[49],"flexibility,":[50],"support":[51],"'big":[53],"data'":[54],"(R's":[55],"long":[56],"vectors),":[57],"ease":[58],"use":[60],"quality":[62],"check":[63],"before":[64],"new":[66],"release.":[67],"These":[68],"changes":[69],"will":[70],"hopefully":[71],"make":[72],"useful":[75],"study":[79],"biodiversity":[81],"evolution":[83],"in":[84],"context":[86],"increasing":[88],"data":[89],"quantity.":[90],"Availability":[91],"implementation:":[93],"is":[95],"distributed":[96],"through":[97],"Comprehensive":[99],"Archive":[101],"Network:":[102],"http://cran.r-project.org/package=ape.":[103],"Further":[104],"information":[105],"may":[106],"be":[107],"found":[108],"at":[109],"http://ape-package.ird.fr/.":[110]},"counts_by_year":[{"year":2026,"cited_by_count":1158},{"year":2025,"cited_by_count":1696},{"year":2024,"cited_by_count":1555},{"year":2023,"cited_by_count":1463},{"year":2022,"cited_by_count":1392},{"year":2021,"cited_by_count":1358},{"year":2020,"cited_by_count":901},{"year":2019,"cited_by_count":288},{"year":2018,"cited_by_count":13},{"year":2016,"cited_by_count":1}],"updated_date":"2026-09-02T18:50:13.731487","created_date":"2025-10-10T00:00:00"}
