{"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":{"id":"doi:10.1515/jib-2023-0051","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0051","pdf_url":null,"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,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1515/jib-2023-0051","any_repository_has_fulltext":true},"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/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"]},{"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"]}],"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"],"raw_orcid":null,"affiliations":[{"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":"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":"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/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"]},{"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"]}],"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"],"raw_orcid":null,"affiliations":[{"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":"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":"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/I182534213","display_name":"Universidade do Porto","ror":"https://ror.org/043pwc612","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213"]},{"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/I4405263123","display_name":"Instituto de Ci\u00eancias Biom\u00e9dicas Albel Salazar","ror":"https://ror.org/02trb6b02","country_code":"PT","type":"education","lineage":["https://openalex.org/I182534213","https://openalex.org/I4405263123"]}],"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"],"raw_orcid":null,"affiliations":[{"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"]},{"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","https://openalex.org/I4405263123"]},{"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"]}]},{"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"],"raw_orcid":null,"affiliations":[{"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 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"]}]},{"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"],"raw_orcid":null,"affiliations":[{"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 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"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5015978945"],"corresponding_institution_ids":["https://openalex.org/I4210158732","https://openalex.org/I4387153674"],"apc_list":{"value":1000,"currency":"EUR","value_usd":1082},"apc_paid":{"value":1000,"currency":"EUR","value_usd":1082},"fwci":0.311,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.55100843,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"21","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9865999817848206,"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":0.9865999817848206,"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":0.9782999753952026,"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":0.9772999882698059,"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":0.9298689961433411},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6240066885948181},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5831570029258728},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5711329579353333},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.5684651732444763},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.4769248366355896},{"id":"https://openalex.org/keywords/computational-phylogenetics","display_name":"Computational phylogenetics","score":0.4720001220703125},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3906903564929962},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.38585364818573},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.36820822954177856},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3388407230377197},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21044257283210754},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1219753623008728},{"id":"https://openalex.org/keywords/clade","display_name":"Clade","score":0.11356523633003235},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.08595061302185059}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.9298689961433411},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6240066885948181},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5831570029258728},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5711329579353333},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.5684651732444763},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.4769248366355896},{"id":"https://openalex.org/C41168302","wikidata":"https://www.wikidata.org/wiki/Q3772859","display_name":"Computational phylogenetics","level":5,"score":0.4720001220703125},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3906903564929962},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.38585364818573},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.36820822954177856},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3388407230377197},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21044257283210754},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1219753623008728},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.11356523633003235},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.08595061302185059}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000096","qualifier_name":"biosynthesis","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001205","descriptor_name":"Ascorbic Acid","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D007313","descriptor_name":"Insecta","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"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":"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":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1515/jib-2023-0051","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0051","pdf_url":null,"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,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39054685","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":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of integrative bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:11377030","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11377030","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11377030/pdf/jib-21-2-jib-2023-0051.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Integr Bioinform","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:cff274ba95d04c47bcf126ae129f29ae","is_oa":true,"landing_page_url":"https://doaj.org/article/cff274ba95d04c47bcf126ae129f29ae","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Integrative Bioinformatics, Vol 21, Iss 2, Pp 1850-60 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2023-0051","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0051","pdf_url":null,"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,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3726528696","display_name":"The novel Drosophila melanogaster ascorbic acid synthesis and transport mechanisms","funder_award_id":"SFRH/BD/145515/2019","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G554081006","display_name":null,"funder_award_id":"2020.00515.CEECIND, SFRH/BD/145515/2019, UIDB/04293/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G647086953","display_name":"Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade","funder_award_id":"UIDB/04293/2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G7392357227","display_name":null,"funder_award_id":"ED431C2018/55-GRC","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G955629214","display_name":null,"funder_award_id":"(2020.00515.CEECIND","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"}],"funders":[{"id":"https://openalex.org/F4320326655","display_name":"Xunta de Galicia","ror":"https://ror.org/0181xnw06"},{"id":"https://openalex.org/F4320334779","display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","ror":"https://ror.org/00snfqn58"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"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/W1532885630","https://openalex.org/W4389053046","https://openalex.org/W2363720861","https://openalex.org/W2800044728","https://openalex.org/W3088015816","https://openalex.org/W2534129866","https://openalex.org/W2057191541","https://openalex.org/W2604174992","https://openalex.org/W2065083790"],"abstract_inverted_index":{"When":[0],"inferring":[1],"the":[2,48,78,90,101,105,124,157,172,175],"evolution":[3,173],"of":[4,44,66,93,104,159,166,174],"a":[5,73,131,149],"gene/gene":[6,106],"family,":[7],"it":[8,58,154],"is":[9,59,168,185],"advisable":[10],"to":[11,27,53,61,72,88,99],"use":[12],"all":[13,31],"available":[14,186],"coding":[15],"sequences":[16,94],"(CDS)":[17],"from":[18],"as":[19,23],"many":[20],"species":[21],"genomes":[22],"possible":[24],"in":[25,86,151,180],"order":[26,87],"infer":[28],"and":[29,34,55,194],"date":[30],"gene":[32],"duplications":[33],"losses.":[35],"Nowadays,":[36],"this":[37],"means":[38],"using":[39,118,138],"hundreds":[40],"or":[41,82,162],"even":[42],"thousands":[43],"CDSs,":[45],"which":[46],"makes":[47],"inferred":[49],"phylogenetic":[50,69],"trees":[51,70],"difficult":[52],"visualize":[54],"interpret.":[56],"Therefore,":[57],"useful":[60],"have":[62],"an":[63],"automated":[64,135],"way":[65],"collapsing":[67,137],"large":[68],"according":[71],"taxonomic":[74,112,139],"term":[75],"decided":[76],"by":[77,146,170],"user":[79],"(family,":[80],"class,":[81],"order,":[83],"for":[84,134],"instance),":[85],"highlight":[89],"minimal":[91],"set":[92],"that":[95,111,114,141],"should":[96],"be":[97,116,143],"used":[98,145],"recapitulate":[100],"full":[102],"history":[103],"family":[107],"being":[108],"studied":[109],"at":[110,187],"level,":[113],"can":[115,142],"refined":[117],"additional":[119],"software.":[120],"Here":[121],"we":[122],"present":[123],"Phylogenetic":[125],"Tree":[126],"Collapser":[127],"(PTC)":[128],"program":[129],"(https://github.com/pegi3s/phylogenetic-tree-collapser),":[130],"flexible":[132],"tool":[133],"tree":[136],"information,":[140],"easily":[144],"researchers":[147],"without":[148],"background":[150],"informatics,":[152],"since":[153],"only":[155],"requires":[156],"installation":[158],"Docker,":[160],"Podman":[161],"Singularity.":[163],"The":[164],"utility":[165],"PTC":[167,192],"demonstrated":[169],"addressing":[171],"ascorbic":[176],"acid":[177],"synthesis":[178],"pathway":[179],"insects.":[181],"A":[182],"Docker":[183,188],"image":[184],"Hub":[189],"(https://hub.docker.com/r/pegi3s/phylogenetic-tree-collapser)":[190],"with":[191],"installed":[193],"ready-to-run.":[195]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
