{"id":"https://openalex.org/W4400958817","doi":"https://doi.org/10.1515/jib-2023-0051","title":"Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information","display_name":"Inferences on the evolution of the ascorbic acid synthesis pathway in insects using Phylogenetic Tree Collapser (PTC), a tool for the automated collapsing of phylogenetic trees using taxonomic information","publication_year":2024,"publication_date":"2024-06-01","ids":{"openalex":"https://openalex.org/W4400958817","doi":"https://doi.org/10.1515/jib-2023-0051","pmid":"https://pubmed.ncbi.nlm.nih.gov/39054685"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0051","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0051/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0051/pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5044007257","display_name":"Daniel Glez\u2010Pe\u00f1a","orcid":"https://orcid.org/0000-0002-6129-7245"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I4210091478","display_name":"Galicia Sur Biomedical Foundation","ror":"https://ror.org/00jdfsf63","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210091478"]},{"id":"https://openalex.org/I4210158352","display_name":"Servicio Gallego de Salud","ror":"https://ror.org/0591s4t67","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210158352"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Daniel Glez-Pe\u00f1a","raw_affiliation_strings":["CINBIO: Centro de Investigaciones Biom\u00e9dicas , University of Vigo , Campus Universitario Lagoas-Marcosende , 36310 , Vigo , Spain","ESEI: Escuela Superior de Ingenier\u00eda Inform\u00e1tica , University of Vigo , Edificio Polit\u00e9cnico, Campus Universitario As Lagoas s/n , 32004 , Ourense , Spain","SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur) , SERGAS-UVIGO , 36213 Vigo , Spain"],"affiliations":[{"raw_affiliation_string":"ESEI: Escuela Superior de Ingenier\u00eda Inform\u00e1tica , University of Vigo , Edificio Polit\u00e9cnico, Campus Universitario As Lagoas s/n , 32004 , Ourense , Spain","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"CINBIO: Centro de Investigaciones Biom\u00e9dicas , University of Vigo , Campus Universitario Lagoas-Marcosende , 36310 , Vigo , Spain","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur) , SERGAS-UVIGO , 36213 Vigo , Spain","institution_ids":["https://openalex.org/I4210091478","https://openalex.org/I4210158352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038155908","display_name":"Hugo L\u00f3pez-Fern\u00e1ndez","orcid":"https://orcid.org/0000-0002-6476-7206"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I4210091478","display_name":"Galicia Sur Biomedical Foundation","ror":"https://ror.org/00jdfsf63","country_code":"ES","type":"other","lineage":["https://openalex.org/I4210091478"]},{"id":"https://openalex.org/I4210158352","display_name":"Servicio Gallego de Salud","ror":"https://ror.org/0591s4t67","country_code":"ES","type":"healthcare","lineage":["https://openalex.org/I4210158352"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Hugo L\u00f3pez-Fern\u00e1ndez","raw_affiliation_strings":["CINBIO: Centro de Investigaciones Biom\u00e9dicas , University of Vigo , Campus Universitario Lagoas-Marcosende , 36310 , Vigo , Spain","ESEI: Escuela Superior de Ingenier\u00eda Inform\u00e1tica , University of Vigo , Edificio Polit\u00e9cnico, Campus Universitario As Lagoas s/n , 32004 , Ourense , Spain","SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur) , SERGAS-UVIGO , 36213 Vigo , Spain"],"affiliations":[{"raw_affiliation_string":"ESEI: Escuela Superior de Ingenier\u00eda Inform\u00e1tica , University of Vigo , Edificio Polit\u00e9cnico, Campus Universitario As Lagoas s/n , 32004 , Ourense , Spain","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"CINBIO: Centro de Investigaciones Biom\u00e9dicas , University of Vigo , Campus Universitario Lagoas-Marcosende , 36310 , Vigo , Spain","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur) , SERGAS-UVIGO , 36213 Vigo , Spain","institution_ids":["https://openalex.org/I4210091478","https://openalex.org/I4210158352"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001885904","display_name":"Pedro Duque","orcid":"https://orcid.org/0000-0001-5782-5036"},"institutions":[{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]},{"id":"https://openalex.org/I4387153674","display_name":"Instituto de Biologia Molecular e Celular","ror":"https://ror.org/005dkht93","country_code":null,"type":"education","lineage":["https://openalex.org/I182534213","https://openalex.org/I4387153674"]},{"id":"https://openalex.org/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Duque","raw_affiliation_strings":["Faculdade de Ci\u00eancias da Universidade do Porto (FCUP) , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal","Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar (ICBAS) , 26706 Universidade do Porto , Rua de Jorge Viterbo Ferreira, 228 , 4050-313 Porto , Portugal","Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S) , 26706 Universidade do Porto , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S) , 26706 Universidade do Porto , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","institution_ids":["https://openalex.org/I4387153674"]},{"raw_affiliation_string":"Instituto de Ci\u00eancias Biom\u00e9dicas Abel Salazar (ICBAS) , 26706 Universidade do Porto , Rua de Jorge Viterbo Ferreira, 228 , 4050-313 Porto , Portugal","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"Faculdade de Ci\u00eancias da Universidade do Porto (FCUP) , Rua do Campo Alegre, s/n , 4169-007 Porto , Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081065000","display_name":"Cristina P. Vieira","orcid":"https://orcid.org/0000-0002-7139-2107"},"institutions":[{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]},{"id":"https://openalex.org/I4387153674","display_name":"Instituto de Biologia Molecular e Celular","ror":"https://ror.org/005dkht93","country_code":null,"type":"education","lineage":["https://openalex.org/I182534213","https://openalex.org/I4387153674"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Cristina P. Vieira","raw_affiliation_strings":["Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S) , 26706 Universidade do Porto , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S) , 26706 Universidade do Porto , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","institution_ids":["https://openalex.org/I4387153674"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015978945","display_name":"Jorge Vieira","orcid":"https://orcid.org/0000-0001-7032-5220"},"institutions":[{"id":"https://openalex.org/I4210158732","display_name":"i3S - Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade, Universidade do Porto","ror":"https://ror.org/04wjk1035","country_code":"PT","type":"facility","lineage":["https://openalex.org/I182534213","https://openalex.org/I4210158732"]},{"id":"https://openalex.org/I4387153674","display_name":"Instituto de Biologia Molecular e Celular","ror":"https://ror.org/005dkht93","country_code":null,"type":"education","lineage":["https://openalex.org/I182534213","https://openalex.org/I4387153674"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"Jorge Vieira","raw_affiliation_strings":["Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S) , 26706 Universidade do Porto , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal"],"affiliations":[{"raw_affiliation_string":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S) , 26706 Universidade do Porto , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","institution_ids":["https://openalex.org/I4210158732"]},{"raw_affiliation_string":"Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208 , 4200-135 Porto , Portugal","institution_ids":["https://openalex.org/I4387153674"]}]}],"institution_assertions":[],"countries_distinct_count":2,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5015978945"],"corresponding_institution_ids":["https://openalex.org/I4210158732","https://openalex.org/I4387153674"],"apc_list":{"value":0,"currency":"USD","value_usd":0,"provenance":"doaj"},"apc_paid":null,"fwci":1.164,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.999978,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":84,"max":92},"biblio":{"volume":"21","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9866,"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":0.9866,"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/T12001","display_name":"Fossil Insects in Amber","score":0.9783,"subfield":{"id":"https://openalex.org/subfields/1105","display_name":"Ecology, Evolution, Behavior and Systematics"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9773,"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/tree","display_name":"Tree (set theory)","score":0.6240067},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.47692484},{"id":"https://openalex.org/keywords/computational-phylogenetics","display_name":"Computational phylogenetics","score":0.47200012}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.929869},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6240067},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.583157},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.57113296},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.5684652},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.47692484},{"id":"https://openalex.org/C41168302","wikidata":"https://www.wikidata.org/wiki/Q3772859","display_name":"Computational phylogenetics","level":5,"score":0.47200012},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39069036},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.38585365},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36820823},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33884072},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21044257},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12197536},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.11356524},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08595061}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0051","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0051/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39054685","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0051","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0051/pdf","source":{"id":"https://openalex.org/S4393917359","display_name":"Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics","issn_l":"1432-4385","issn":["1432-4385","1613-4516"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[{"funder":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia","award_id":"ED431C2018/55-GRC"},{"funder":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award_id":"2020.00515.CEECIND, SFRH/BD/145515/2019, UIDB/04293/2020"}],"datasets":[],"versions":[],"referenced_works_count":45,"referenced_works":["https://openalex.org/W1841334989","https://openalex.org/W1969375160","https://openalex.org/W1988316620","https://openalex.org/W1994589056","https://openalex.org/W2004575303","https://openalex.org/W2005937606","https://openalex.org/W2019216543","https://openalex.org/W2031611770","https://openalex.org/W2044364290","https://openalex.org/W2044579739","https://openalex.org/W2055765155","https://openalex.org/W2057250770","https://openalex.org/W2059359550","https://openalex.org/W2065016714","https://openalex.org/W2077046836","https://openalex.org/W2079375310","https://openalex.org/W2127322768","https://openalex.org/W2131725930","https://openalex.org/W2132926880","https://openalex.org/W2134415959","https://openalex.org/W2144345157","https://openalex.org/W2148698435","https://openalex.org/W2152207030","https://openalex.org/W2161975983","https://openalex.org/W2185005392","https://openalex.org/W2228668600","https://openalex.org/W2400909259","https://openalex.org/W2613409207","https://openalex.org/W2745884621","https://openalex.org/W2802996424","https://openalex.org/W2902640907","https://openalex.org/W2950907524","https://openalex.org/W2977870980","https://openalex.org/W2988396470","https://openalex.org/W2998746673","https://openalex.org/W3109654795","https://openalex.org/W3127212423","https://openalex.org/W3136433687","https://openalex.org/W3184501373","https://openalex.org/W3198187693","https://openalex.org/W4251491798","https://openalex.org/W4251751280","https://openalex.org/W4283519055","https://openalex.org/W4285563069","https://openalex.org/W4383752005"],"related_works":["https://openalex.org/W85430217","https://openalex.org/W4389053046","https://openalex.org/W3088015816","https://openalex.org/W2800044728","https://openalex.org/W2604174992","https://openalex.org/W2534129866","https://openalex.org/W2363720861","https://openalex.org/W2065083790","https://openalex.org/W2057191541","https://openalex.org/W1532885630"],"abstract_inverted_index":{"Abstract":[0],"When":[1],"inferring":[2],"the":[3,49,79,91,102,106,125,160,175,178],"evolution":[4,176],"of":[5,45,67,94,105,162,169,177],"a":[6,74,134,152],"gene/gene":[7,107],"family,":[8],"it":[9,59,157],"is":[10,60,171,188],"advisable":[11],"to":[12,28,54,62,73,89,100],"use":[13],"all":[14,32],"available":[15,189],"coding":[16],"sequences":[17,95],"(CDS)":[18],"from":[19],"as":[20,24],"many":[21],"species":[22],"genomes":[23],"possible":[25],"in":[26,87,154,183],"order":[27,88],"infer":[29],"and":[30,35,56,199],"date":[31],"gene":[33],"duplications":[34],"losses.":[36],"Nowadays,":[37],"this":[38],"means":[39],"using":[40,119,141],"hundreds":[41],"or":[42,83,165],"even":[43],"thousands":[44],"CDSs,":[46],"which":[47],"makes":[48],"inferred":[50],"phylogenetic":[51,70],"trees":[52,71],"difficult":[53],"visualize":[55],"interpret.":[57],"Therefore,":[58],"useful":[61],"have":[63],"an":[64],"automated":[65,138],"way":[66],"collapsing":[68,140],"large":[69],"according":[72],"taxonomic":[75,113,142],"term":[76],"decided":[77],"by":[78,149,173],"user":[80],"(family,":[81],"class,":[82],"order,":[84],"for":[85,137],"instance),":[86],"highlight":[90],"minimal":[92],"set":[93],"that":[96,112,115,144],"should":[97],"be":[98,117,146],"used":[99,148],"recapitulate":[101],"full":[103],"history":[104],"family":[108],"being":[109],"studied":[110],"at":[111,190],"level,":[114],"can":[116,145],"refined":[118],"additional":[120],"software.":[121],"Here":[122],"we":[123],"present":[124],"Phylogenetic":[126],"Tree":[127],"Collapser":[128],"(PTC)":[129],"program":[130],"(":[131,193],"https://github.com/pegi3s/phylogenetic-tree-collapser":[132],"),":[133],"flexible":[135],"tool":[136],"tree":[139],"information,":[143],"easily":[147],"researchers":[150],"without":[151],"background":[153],"informatics,":[155],"since":[156],"only":[158],"requires":[159],"installation":[161],"Docker,":[163],"Podman":[164],"Singularity.":[166],"The":[167],"utility":[168],"PTC":[170,197],"demonstrated":[172],"addressing":[174],"ascorbic":[179],"acid":[180],"synthesis":[181],"pathway":[182],"insects.":[184],"A":[185],"Docker":[186,191],"image":[187],"Hub":[192],"https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser":[194],")":[195],"with":[196],"installed":[198],"ready-to-run.":[200]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W4400958817","counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2025-01-04T03:09:16.750895","created_date":"2024-07-25"}