{"id":"https://openalex.org/W4398796180","doi":"https://doi.org/10.21105/joss.06943","title":"DendroPy 5: a mature Python library for phylogeneticcomputing","display_name":"DendroPy 5: a mature Python library for phylogeneticcomputing","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4398796180","doi":"https://doi.org/10.21105/joss.06943"},"language":"en","primary_location":{"id":"doi:10.21105/joss.06943","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.06943","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.06943.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"type":"preprint","indexed_in":["arxiv","crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.06943.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041111645","display_name":"Matthew Andres Moreno","orcid":"https://orcid.org/0000-0003-4726-4479"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Matthew Andres Moreno","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4726-4479","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021006859","display_name":"Mark T. Holder","orcid":"https://orcid.org/0000-0001-5575-0536"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mark T. Holder","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-5575-0536","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5008542908","display_name":"Jeet Sukumaran","orcid":"https://orcid.org/0000-0002-9222-9608"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jeet Sukumaran","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-9222-9608","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5041111645"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":6.5583,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.97594677,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"9","issue":"101","first_page":"6943","last_page":"6943"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9994000196456909,"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":0.9994000196456909,"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":0.980400025844574,"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/T12946","display_name":"Fractal and DNA sequence analysis","score":0.9682999849319458,"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/python","display_name":"Python (programming language)","score":0.6619017124176025},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4790003001689911},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.47842031717300415},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.44179320335388184},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4383716881275177},{"id":"https://openalex.org/keywords/phylogeography","display_name":"Phylogeography","score":0.4152885377407074},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.29925376176834106},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19045361876487732}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6619017124176025},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4790003001689911},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.47842031717300415},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.44179320335388184},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4383716881275177},{"id":"https://openalex.org/C94043034","wikidata":"https://www.wikidata.org/wiki/Q377756","display_name":"Phylogeography","level":4,"score":0.4152885377407074},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.29925376176834106},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19045361876487732},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.21105/joss.06943","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.06943","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.06943.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},{"id":"pmh:oai:arXiv.org:2405.14120","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2405.14120","pdf_url":"https://arxiv.org/pdf/2405.14120","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"}],"best_oa_location":{"id":"doi:10.21105/joss.06943","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.06943","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.06943.pdf","source":{"id":"https://openalex.org/S4210214273","display_name":"The Journal of Open Source Software","issn_l":"2475-9066","issn":["2475-9066"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315853","host_organization_name":"Open Journals","host_organization_lineage":["https://openalex.org/P4310315853"],"host_organization_lineage_names":["Open Journals"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Open Source Software","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure","score":0.6100000143051147}],"awards":[{"id":"https://openalex.org/G2673034252","display_name":null,"funder_award_id":"1457776","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4322358350","display_name":"COLLABORATIVE RESEARCH: Phylogenomics, spatial phylogenetics and conservation prioritization in trapdoor spiders (and kin) of the California Floristic Province","funder_award_id":"1937725","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4398796180.pdf","grobid_xml":"https://content.openalex.org/works/W4398796180.grobid-xml"},"referenced_works_count":42,"referenced_works":["https://openalex.org/W17481062","https://openalex.org/W1998846911","https://openalex.org/W2005946215","https://openalex.org/W2026062398","https://openalex.org/W2029195137","https://openalex.org/W2100412820","https://openalex.org/W2102424972","https://openalex.org/W2113708808","https://openalex.org/W2114850508","https://openalex.org/W2119837484","https://openalex.org/W2127431120","https://openalex.org/W2139736670","https://openalex.org/W2141052558","https://openalex.org/W2143980572","https://openalex.org/W2148698435","https://openalex.org/W2152546486","https://openalex.org/W2166655850","https://openalex.org/W2170041483","https://openalex.org/W2277953252","https://openalex.org/W2533812722","https://openalex.org/W2809191014","https://openalex.org/W2883251903","https://openalex.org/W2950407147","https://openalex.org/W2952454337","https://openalex.org/W2952894864","https://openalex.org/W3009335848","https://openalex.org/W3163112933","https://openalex.org/W3173893761","https://openalex.org/W3197138076","https://openalex.org/W3205637413","https://openalex.org/W4284879653","https://openalex.org/W4285805324","https://openalex.org/W4311635366","https://openalex.org/W4321611856","https://openalex.org/W4323669978","https://openalex.org/W4384616649","https://openalex.org/W4386902858","https://openalex.org/W4387631145","https://openalex.org/W4392028301","https://openalex.org/W4393107044","https://openalex.org/W4396987478","https://openalex.org/W6950177912"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W2170393268","https://openalex.org/W2144958703","https://openalex.org/W2080410528","https://openalex.org/W4246848024","https://openalex.org/W2029134973","https://openalex.org/W2529820324"],"abstract_inverted_index":{"Shahbandegan":[0],"et":[1],"al.,":[2],"2022),":[3],"and":[4,7,25,41,101,131,136],"beyond.High-throughput":[5],"genetic":[6],"phenotypic":[8],"data":[9],"has":[10,58],"realized":[11],"groundbreaking":[12],"results,":[13],"in":[14,33,56,63,92,116],"large":[15],"part,":[16],"through":[17],"conjunction":[18],"with":[19],"open-source":[20],"software":[21,39,86,132,140],"used":[22],"to":[23,96,109],"process":[24],"analyze":[26],"it.Indeed,":[27],"the":[28,43,50,65,75,80,94,145],"preceding":[29],"decades":[30],"have":[31],"ushered":[32],"a":[34,60,89,97,112,124],"flourishing":[35],"ecosystem":[36,126],"of":[37,45,79,120,127],"bioinformatics":[38,66,135],"applications":[40],"libraries.Over":[42],"course":[44],"its":[46],"nearly":[47],"fifteen-year":[48],"history,":[49],"DendroPy":[51,82,108],"library":[52,95],"for":[53,153],"phylogenetic":[54],"computation":[55],"Python":[57],"established":[59],"generalist":[61],"niche":[62],"serving":[64],"community":[67],"(Sukumaran":[68],"&":[69],"Holder,":[70],"2010).Here,":[71],"we":[72],"report":[73],"on":[74],"recent":[76],"major":[77,90,147],"release":[78,87],"library,":[81],"version":[83],"5.":[84],"The":[85],"represents":[88],"milestone":[91],"transitioning":[93],"sustainable":[98],"long-term":[99],"development":[100],"maintenance":[102],"trajectory.As":[103],"such,":[104],"this":[105],"work":[106],"positions":[107],"continue":[110],"fulfilling":[111],"key":[113],"supporting":[114,134],"role":[115],"phyloinformatics":[117],"infrastructure.":[118],"Statement":[119],"NeedDendroPy":[121],"operates":[122],"within":[123],"rich":[125],"packages,":[128],"frameworks,":[129],"toolkits,":[130],"projects":[133],"phylogenetics":[137],"research.The":[138],"broader":[139],"landscape":[141],"largely":[142],"divides":[143],"into":[144],"following":[146],"categories,":[148],"1.":[149],"High-performance":[150],"specialized":[151],"tools":[152],"inference":[154],"(e.g.,":[155]},"counts_by_year":[{"year":2026,"cited_by_count":11},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":1}],"updated_date":"2026-05-22T09:01:20.584952","created_date":"2025-10-10T00:00:00"}
