{"id":"https://openalex.org/W4415608691","doi":"https://doi.org/10.21105/joss.09040","title":"phylo2vec: a library for vector-based phylogenetic tree manipulation","display_name":"phylo2vec: a library for vector-based phylogenetic tree manipulation","publication_year":2025,"publication_date":"2025-10-28","ids":{"openalex":"https://openalex.org/W4415608691","doi":"https://doi.org/10.21105/joss.09040"},"language":null,"primary_location":{"id":"doi:10.21105/joss.09040","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.09040","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.09040.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":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://joss.theoj.org/papers/10.21105/joss.09040.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055084920","display_name":"Neil Scheidwasser","orcid":"https://orcid.org/0000-0001-9922-0289"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I1320355602","display_name":"Statistics Denmark","ror":"https://ror.org/000f7jy90","country_code":"DK","type":"government","lineage":["https://openalex.org/I1320355602"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Neil Scheidwasser","raw_affiliation_strings":["Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-9922-0289","affiliations":[{"raw_affiliation_string":"Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I1320355602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110125640","display_name":"Asish C. Nag","orcid":"https://orcid.org/0009-0008-1790-597X"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ayush Nag","raw_affiliation_strings":["eScience Institute, University of Washington, Seattle, United States"],"raw_orcid":"https://orcid.org/0009-0008-1790-597X","affiliations":[{"raw_affiliation_string":"eScience Institute, University of Washington, Seattle, United States","institution_ids":["https://openalex.org/I58610484","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028742823","display_name":"Matthew J. Penn","orcid":"https://orcid.org/0000-0001-8682-5393"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I1320355602","display_name":"Statistics Denmark","ror":"https://ror.org/000f7jy90","country_code":"DK","type":"government","lineage":["https://openalex.org/I1320355602"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Matthew J. Penn","raw_affiliation_strings":["Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0000-0001-8682-5393","affiliations":[{"raw_affiliation_string":"Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I1320355602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052190734","display_name":"Anthony M.V. Jakob","orcid":"https://orcid.org/0000-0002-0996-1356"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anthony Jakob","raw_affiliation_strings":["Independent researcher"],"raw_orcid":"https://orcid.org/0000-0002-0996-1356","affiliations":[{"raw_affiliation_string":"Independent researcher","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111133104","display_name":"Frederik M\u00f8lkj\u00e6r Andersen","orcid":"https://orcid.org/0009-0004-4071-3707"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I1320355602","display_name":"Statistics Denmark","ror":"https://ror.org/000f7jy90","country_code":"DK","type":"government","lineage":["https://openalex.org/I1320355602"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Frederik M\u00f8lkj\u00e6r Andersen","raw_affiliation_strings":["Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0009-0004-4071-3707","affiliations":[{"raw_affiliation_string":"Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I1320355602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031671404","display_name":"Mark P. Khurana","orcid":"https://orcid.org/0000-0002-1123-7674"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I1320355602","display_name":"Statistics Denmark","ror":"https://ror.org/000f7jy90","country_code":"DK","type":"government","lineage":["https://openalex.org/I1320355602"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"Mark Poulsen Khurana","raw_affiliation_strings":["Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-1123-7674","affiliations":[{"raw_affiliation_string":"Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I1320355602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119789413","display_name":"Landung Setiawan","orcid":"https://orcid.org/0000-0002-1624-2667"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]},{"id":"https://openalex.org/I58610484","display_name":"Seattle University","ror":"https://ror.org/02jqc0m91","country_code":"US","type":"education","lineage":["https://openalex.org/I58610484"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Landung Setiawan","raw_affiliation_strings":["eScience Institute, University of Washington, Seattle, United States"],"raw_orcid":"https://orcid.org/0000-0002-1624-2667","affiliations":[{"raw_affiliation_string":"eScience Institute, University of Washington, Seattle, United States","institution_ids":["https://openalex.org/I58610484","https://openalex.org/I201448701"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022291539","display_name":"David A. Duch\u00eane","orcid":"https://orcid.org/0000-0002-5479-1974"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I1320355602","display_name":"Statistics Denmark","ror":"https://ror.org/000f7jy90","country_code":"DK","type":"government","lineage":["https://openalex.org/I1320355602"]}],"countries":["DK"],"is_corresponding":false,"raw_author_name":"David A. Duch\u00eane","raw_affiliation_strings":["Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-5479-1974","affiliations":[{"raw_affiliation_string":"Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I1320355602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091290326","display_name":"Samir Bhatt","orcid":"https://orcid.org/0000-0002-0891-4611"},"institutions":[{"id":"https://openalex.org/I124055696","display_name":"University of Copenhagen","ror":"https://ror.org/035b05819","country_code":"DK","type":"education","lineage":["https://openalex.org/I124055696"]},{"id":"https://openalex.org/I1320355602","display_name":"Statistics Denmark","ror":"https://ror.org/000f7jy90","country_code":"DK","type":"government","lineage":["https://openalex.org/I1320355602"]},{"id":"https://openalex.org/I47508984","display_name":"Imperial College London","ror":"https://ror.org/041kmwe10","country_code":"GB","type":"education","lineage":["https://openalex.org/I47508984"]}],"countries":["DK","GB"],"is_corresponding":false,"raw_author_name":"Samir Bhatt","raw_affiliation_strings":["MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom","Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark"],"raw_orcid":"https://orcid.org/0000-0002-0891-4611","affiliations":[{"raw_affiliation_string":"MRC Centre for Global Infectious Disease Analysis, Imperial College London, London, United Kingdom","institution_ids":["https://openalex.org/I47508984"]},{"raw_affiliation_string":"Section of Health Data Science and AI, University of Copenhagen, Copenhagen, Denmark","institution_ids":["https://openalex.org/I124055696","https://openalex.org/I1320355602"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":9,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.576,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.71774335,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"10","issue":"114","first_page":"9040","last_page":"9040"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8050000071525574,"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":0.8050000071525574,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.06400000303983688,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.008799999952316284,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.7789000272750854},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5942000150680542},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.3643999993801117},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.349700003862381},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.34869998693466187}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7789000272750854},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5942000150680542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49810001254081726},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4399000108242035},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.3653999865055084},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.3643999993801117},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.349700003862381},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.34869998693466187},{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.34389999508857727},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3391999900341034},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3061999976634979},{"id":"https://openalex.org/C2992072516","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetic relationship","level":4,"score":0.25130000710487366}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.21105/joss.09040","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.09040","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.09040.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"}],"best_oa_location":{"id":"doi:10.21105/joss.09040","is_oa":true,"landing_page_url":"https://doi.org/10.21105/joss.09040","pdf_url":"https://joss.theoj.org/papers/10.21105/joss.09040.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":[],"awards":[{"id":"https://openalex.org/G551833079","display_name":null,"funder_award_id":"NNF20OC0059309","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"},{"id":"https://openalex.org/G6207269621","display_name":null,"funder_award_id":"DNRF160","funder_id":"https://openalex.org/F4320320943","funder_display_name":"Danmarks Grundforskningsfond"},{"id":"https://openalex.org/G6492113386","display_name":"MRC Centre for Global Infectious Disease Analysis (MRC GIDA)","funder_award_id":"MR/X020258/1","funder_id":"https://openalex.org/F4320334626","funder_display_name":"Medical Research Council"},{"id":"https://openalex.org/G8537180282","display_name":null,"funder_award_id":"NNF20OC0059309","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G8537797102","display_name":null,"funder_award_id":"NNF23OC0084647","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"}],"funders":[{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320320943","display_name":"Danmarks Grundforskningsfond","ror":"https://ror.org/00znyv691"},{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"},{"id":"https://openalex.org/F4320334626","display_name":"Medical Research Council","ror":"https://ror.org/03x94j517"},{"id":"https://openalex.org/F4320338462","display_name":"European and Developing Countries Clinical Trials Partnership","ror":"https://ror.org/031jv9v19"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4415608691.pdf","grobid_xml":"https://content.openalex.org/works/W4415608691.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1991156902","https://openalex.org/W2062962705","https://openalex.org/W2066354072","https://openalex.org/W2136485386","https://openalex.org/W2151328554","https://openalex.org/W2169981472","https://openalex.org/W2245493112","https://openalex.org/W2277953252","https://openalex.org/W2803902276","https://openalex.org/W2883251903","https://openalex.org/W2912430686","https://openalex.org/W3025857586","https://openalex.org/W3160568774","https://openalex.org/W4200322511","https://openalex.org/W4224216303","https://openalex.org/W4250847479","https://openalex.org/W4308963287","https://openalex.org/W4323037726","https://openalex.org/W4363675392","https://openalex.org/W4389628279","https://openalex.org/W4391539704","https://openalex.org/W4398796180","https://openalex.org/W4400140878","https://openalex.org/W4401729200","https://openalex.org/W4407722258","https://openalex.org/W4407760641","https://openalex.org/W6910419080"],"related_works":[],"abstract_inverted_index":{"Compared":[0],"to":[1,22,40],"the":[2,24],"traditional":[3],"Newick":[4],"format":[5],"which":[6],"represents":[7],"trees":[8],"using":[9],"strings":[10],"of":[11],"nested":[12],"parentheses":[13],"(Felsenstein,":[14],"2004),":[15],"modern":[16],"tree":[17,25],"representations":[18],"utilise":[19],"integer":[20],"vectors":[21],"define":[23],"topology":[26],"traversal.This":[27],"approach":[28],"offers":[29],"several":[30],"advantages,":[31],"including":[32],"easier":[33],"manipulation,":[34],"increased":[35],"memory":[36],"efficiency,":[37],"and":[38],"applicability":[39],"machine":[41],"learning.":[42]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-28T00:00:00"}
