{"id":"https://openalex.org/W2119552198","doi":"https://doi.org/10.1093/bioinformatics/bts184","title":"ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R","display_name":"ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R","publication_year":2012,"publication_date":"2012-04-11","ids":{"openalex":"https://openalex.org/W2119552198","doi":"https://doi.org/10.1093/bioinformatics/bts184","mag":"2119552198","pmid":"https://pubmed.ncbi.nlm.nih.gov/22495750"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts184","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts184","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1536/48867925/bioinformatics_28_11_1536.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/28/11/1536/48867925/bioinformatics_28_11_1536.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085504892","display_name":"Andrei-Alin Popescu","orcid":null},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Andrei-Alin Popescu","raw_affiliation_strings":["1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226/5554 \u2013 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia"],"affiliations":[{"raw_affiliation_string":"1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226/5554 \u2013 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia","institution_ids":["https://openalex.org/I1118541","https://openalex.org/I2799300731"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007694498","display_name":"Katharina T. Huber","orcid":"https://orcid.org/0000-0002-6368-7511"},"institutions":[{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Katharina T. Huber","raw_affiliation_strings":["1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226/5554 \u2013 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia"],"affiliations":[{"raw_affiliation_string":"1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226/5554 \u2013 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia","institution_ids":["https://openalex.org/I1118541","https://openalex.org/I2799300731"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091069787","display_name":"Emmanuel Paradis","orcid":"https://orcid.org/0000-0003-3092-2199"},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I1118541","display_name":"University of East Anglia","ror":"https://ror.org/026k5mg93","country_code":"GB","type":"education","lineage":["https://openalex.org/I1118541"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Emmanuel Paradis","raw_affiliation_strings":["1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226/5554 \u2013 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia"],"affiliations":[{"raw_affiliation_string":"1 School of Computing Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK and 2Institut des Sciences de l'\u00c9volution, Institut de Recherche pour le D\u00e9veloppement, ISEM UMR 226/5554 \u2013 UM2/CNRS/IRD, Jl. Taman Kemang 32B, Jakarta 12730, Indonesia","institution_ids":["https://openalex.org/I1118541","https://openalex.org/I2799300731"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085504892"],"corresponding_institution_ids":["https://openalex.org/I1118541","https://openalex.org/I2799300731"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.3029,"has_fulltext":false,"cited_by_count":310,"citation_normalized_percentile":{"value":0.9526739,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"28","issue":"11","first_page":"1536","last_page":"1537"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9973000288009644,"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":0.9973000288009644,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9793999791145325,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9789000153541565,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7446051836013794},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.599841833114624},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5227825045585632},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4954270124435425},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.48991960287094116},{"id":"https://openalex.org/keywords/distance-matrices-in-phylogeny","display_name":"Distance matrices in phylogeny","score":0.44011884927749634},{"id":"https://openalex.org/keywords/distance-matrix","display_name":"Distance matrix","score":0.43708378076553345},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.42895859479904175},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4287119209766388},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.41912710666656494},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.35691890120506287},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.32512539625167847},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31265440583229065},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22149884700775146},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2201860249042511},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.17119890451431274},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13039860129356384},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10969963669776917}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7446051836013794},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.599841833114624},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5227825045585632},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4954270124435425},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.48991960287094116},{"id":"https://openalex.org/C5349765","wikidata":"https://www.wikidata.org/wiki/Q5282866","display_name":"Distance matrices in phylogeny","level":2,"score":0.44011884927749634},{"id":"https://openalex.org/C111208986","wikidata":"https://www.wikidata.org/wiki/Q901698","display_name":"Distance matrix","level":2,"score":0.43708378076553345},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.42895859479904175},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4287119209766388},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.41912710666656494},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.35691890120506287},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.32512539625167847},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31265440583229065},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22149884700775146},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2201860249042511},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.17119890451431274},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13039860129356384},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10969963669776917},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bts184","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts184","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1536/48867925/bioinformatics_28_11_1536.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:22495750","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22495750","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:10.1.1.876.8536","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.876.8536","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/content/early/2012/04/06/bioinformatics.bts184.full.pdf","raw_type":"text"},{"id":"pmh:oai:HAL:hal-01822119v1","is_oa":false,"landing_page_url":"https://hal.science/hal-01822119","pdf_url":null,"source":{"id":"https://openalex.org/S4406922466","display_name":"SPIRE - Sciences Po Institutional REpository","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2012, 28 (11), pp.1536 - 1537. &#x27E8;10.1093/bioinformatics/bts184&#x27E9;","raw_type":"Journal articles"},{"id":"pmh:oai:ueaeprints.uea.ac.uk:39667","is_oa":false,"landing_page_url":"https://ueaeprints.uea.ac.uk/id/eprint/39667/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400384","display_name":"UEA Digital Repository (University of East Anglia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1118541","host_organization_name":"University of East Anglia","host_organization_lineage":["https://openalex.org/I1118541"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts184","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts184","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/11/1536/48867925/bioinformatics_28_11_1536.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/W2119552198.pdf","grobid_xml":"https://content.openalex.org/works/W2119552198.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1990157150","https://openalex.org/W1996835973","https://openalex.org/W2016488737","https://openalex.org/W2046837061","https://openalex.org/W2092493619","https://openalex.org/W2095724872","https://openalex.org/W2097706568","https://openalex.org/W2120819924","https://openalex.org/W2127166992","https://openalex.org/W2132926880","https://openalex.org/W2144362290","https://openalex.org/W2150003885","https://openalex.org/W2151409320","https://openalex.org/W2151690408","https://openalex.org/W2207526553","https://openalex.org/W2328415730","https://openalex.org/W2582743722","https://openalex.org/W4285719527","https://openalex.org/W4388212639","https://openalex.org/W6674647444"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2001076853","https://openalex.org/W1872375678","https://openalex.org/W2057191541","https://openalex.org/W2883025420","https://openalex.org/W4387171312","https://openalex.org/W1992658754","https://openalex.org/W4388316203","https://openalex.org/W2111939425","https://openalex.org/W2065083790"],"abstract_inverted_index":{"ape":[0],"is":[1],"distributed":[2],"through":[3],"the":[4],"Comprehensive":[5],"R":[6],"Archive":[7],"Network:":[8],"http://cran.r-project.org/web/packages/ape/index.html":[9],"Further":[10],"information":[11],"may":[12],"be":[13],"found":[14],"at":[15],"http://ape.mpl.ird.fr/pegas/":[16]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":14},{"year":2022,"cited_by_count":24},{"year":2021,"cited_by_count":27},{"year":2020,"cited_by_count":39},{"year":2019,"cited_by_count":45},{"year":2018,"cited_by_count":60},{"year":2017,"cited_by_count":28},{"year":2016,"cited_by_count":13},{"year":2015,"cited_by_count":14},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":8}],"updated_date":"2026-04-18T07:56:08.524223","created_date":"2025-10-10T00:00:00"}
