{"id":"https://openalex.org/W4393200374","doi":"https://doi.org/10.1515/jib-2023-0046","title":"Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites","display_name":"Auto-phylo v2 and auto-phylo-pipeliner: building advanced, flexible, and reusable pipelines for phylogenetic inferences, estimation of variability levels and identification of positively selected amino acid sites","publication_year":2024,"publication_date":"2024-03-26","ids":{"openalex":"https://openalex.org/W4393200374","doi":"https://doi.org/10.1515/jib-2023-0046","pmid":"https://pubmed.ncbi.nlm.nih.gov/38529929"},"language":"en","primary_location":{"id":"doi:10.1515/jib-2023-0046","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0046","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0046/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,"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://www.degruyter.com/document/doi/10.1515/jib-2023-0046/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","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, Department of Computer Science, ESEI\u2014Escuela Superior de Ingenier\u00eda Inform\u00e1tica , Universidade de Vigo , 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, Department of Computer Science, ESEI\u2014Escuela Superior de Ingenier\u00eda Inform\u00e1tica , Universidade de Vigo , 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/A5081628209","display_name":"Miguel Pinto","orcid":"https://orcid.org/0000-0002-9031-4577"},"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"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Pinto","raw_affiliation_strings":["26706 Faculdade de Ci\u00eancias da Universidade do Porto (FCUP) , Rua do Campo Alegre, s/n, 4169-007 Porto , Portugal","26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"26706 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":"26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), 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":["26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal","Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), 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":"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"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Duque","raw_affiliation_strings":["26706 Faculdade de Ci\u00eancias da Universidade do Porto (FCUP) , Rua do Campo Alegre, s/n, 4169-007 Porto , Portugal","26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal","Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal","School of Medicine and Biomedical Sciences (ICBAS) , Porto University , Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto , Portugal","School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"26706 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":"26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), 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":"School of Medicine and Biomedical Sciences (ICBAS) , Porto University , Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto , Portugal","institution_ids":["https://openalex.org/I182534213"]},{"raw_affiliation_string":"School of Medicine and Biomedical Sciences (ICBAS), Porto University, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal","institution_ids":["https://openalex.org/I182534213"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026022133","display_name":"Miguel Reboiro\u2010Jato","orcid":"https://orcid.org/0000-0001-8749-2703"},"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":"Miguel Reboiro-Jato","raw_affiliation_strings":["CINBIO, Department of Computer Science, ESEI\u2014Escuela Superior de Ingenier\u00eda Inform\u00e1tica , Universidade de Vigo , 32004 Ourense , Spain","SING Research Group , Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO , 36213 Vigo , Spain"],"raw_orcid":"https://orcid.org/0000-0001-8749-2703","affiliations":[{"raw_affiliation_string":"CINBIO, Department of Computer Science, ESEI\u2014Escuela Superior de Ingenier\u00eda Inform\u00e1tica , Universidade de Vigo , 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":"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":["26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), Universidade do Porto , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal","Instituto de Biologia Molecular e Celular (IBMC) , Rua Alfredo Allen, 208, 4200-135 Porto , Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"26706 Instituto de Investiga\u00e7\u00e3o e Inova\u00e7\u00e3o em Sa\u00fade (I3S), 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"]}]}],"institutions":[],"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":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":0.53309609,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":97,"max":98},"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/T11927","display_name":"Plant Reproductive Biology","score":0.9990000128746033,"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/T11927","display_name":"Plant Reproductive Biology","score":0.9990000128746033,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9980000257492065,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9965000152587891,"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/identification","display_name":"Identification (biology)","score":0.5788660049438477},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5672924518585205},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5661726593971252},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.542540431022644},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.5299711227416992},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.48661836981773376},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45258790254592896},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.4450833797454834},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3969150185585022},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37038594484329224},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3251320421695709},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.32128673791885376},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1236419677734375},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.0982365608215332},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09729698300361633}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5788660049438477},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5672924518585205},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5661726593971252},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.542540431022644},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.5299711227416992},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.48661836981773376},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45258790254592896},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.4450833797454834},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3969150185585022},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37038594484329224},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3251320421695709},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.32128673791885376},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1236419677734375},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0982365608215332},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09729698300361633}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D000596","descriptor_name":"Amino Acids","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"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":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1515/jib-2023-0046","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0046","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0046/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,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38529929","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38529929","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:11378518","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11378518","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11378518/pdf/jib-21-2-jib-2023-0046.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:147ee1c36fed406baf544d6474744a6d","is_oa":true,"landing_page_url":"https://doaj.org/article/147ee1c36fed406baf544d6474744a6d","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 2466-74 (2024)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1515/jib-2023-0046","is_oa":true,"landing_page_url":"https://doi.org/10.1515/jib-2023-0046","pdf_url":"https://www.degruyter.com/document/doi/10.1515/jib-2023-0046/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,"raw_source_name":"Journal of Integrative Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1496055848","display_name":null,"funder_award_id":"ED431C","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"id":"https://openalex.org/G289314026","display_name":null,"funder_award_id":"ED431C 2022/03-GRC","funder_id":"https://openalex.org/F4320326655","funder_display_name":"Xunta de Galicia"},{"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/G3821492978","display_name":null,"funder_award_id":"ED431C 2022/03-GRC","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4316116677","display_name":null,"funder_award_id":"NORTE2020","funder_id":"https://openalex.org/F4320334779","funder_display_name":"Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia"},{"id":"https://openalex.org/G4718743385","display_name":null,"funder_award_id":"ED431C 2022/03-GRC","funder_id":"https://openalex.org/F4320325108","funder_display_name":"Conseller\u00eda de Cultura, Educaci\u00f3n e Ordenaci\u00f3n Universitaria, Xunta de Galicia"},{"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"}],"funders":[{"id":"https://openalex.org/F4320325108","display_name":"Conseller\u00eda de Cultura, Educaci\u00f3n e Ordenaci\u00f3n Universitaria, Xunta de Galicia","ror":"https://ror.org/03gq5rs15"},{"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":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4393200374.pdf","grobid_xml":"https://content.openalex.org/works/W4393200374.grobid-xml"},"referenced_works_count":43,"referenced_works":["https://openalex.org/W1560719351","https://openalex.org/W1982372752","https://openalex.org/W1996423252","https://openalex.org/W2007278634","https://openalex.org/W2012387546","https://openalex.org/W2021307371","https://openalex.org/W2034239482","https://openalex.org/W2076554224","https://openalex.org/W2087741523","https://openalex.org/W2105329815","https://openalex.org/W2106882534","https://openalex.org/W2108512869","https://openalex.org/W2127774996","https://openalex.org/W2132926880","https://openalex.org/W2136872570","https://openalex.org/W2140872496","https://openalex.org/W2144362290","https://openalex.org/W2153868426","https://openalex.org/W2158597791","https://openalex.org/W2170565120","https://openalex.org/W2171436024","https://openalex.org/W2186453591","https://openalex.org/W2189708363","https://openalex.org/W2279324994","https://openalex.org/W2323678688","https://openalex.org/W2327470758","https://openalex.org/W2743986353","https://openalex.org/W2802282671","https://openalex.org/W2911390449","https://openalex.org/W2942705209","https://openalex.org/W3109654795","https://openalex.org/W3157396199","https://openalex.org/W3160039807","https://openalex.org/W3166010131","https://openalex.org/W3198187693","https://openalex.org/W4214514396","https://openalex.org/W4280589997","https://openalex.org/W4297851063","https://openalex.org/W4307371372","https://openalex.org/W4310711967","https://openalex.org/W4324376625","https://openalex.org/W4382631007","https://openalex.org/W4383752005"],"related_works":["https://openalex.org/W2132972885","https://openalex.org/W4248019281","https://openalex.org/W2064153754","https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2739032002","https://openalex.org/W2133116680","https://openalex.org/W2091678889"],"abstract_inverted_index":{"Abstract":[0],"The":[1],"vast":[2],"amount":[3],"of":[4,57,84,93,95,103,143,160],"genome":[5,41],"sequence":[6,79],"data":[7],"that":[8,12,136,181],"is":[9,13],"available,":[10],"and":[11,59,62,97,100,141,156,195],"predicted":[14],"to":[15,112,120,173],"drastically":[16],"increase":[17],"in":[18,183,198],"the":[19,33,55,82,91,101,139,158],"near":[20],"future,":[21],"can":[22],"only":[23],"be":[24],"efficiently":[25],"dealt":[26],"with":[27],"by":[28],"building":[29],"automated":[30],"pipelines.":[31,145],"Indeed,":[32],"Earth":[34],"Biogenome":[35],"Project":[36],"will":[37],"produce":[38],"high-quality":[39],"reference":[40,85],"sequences":[42,196],"for":[43,70,152,157],"all":[44],"1.8":[45],"million":[46],"named":[47],"living":[48],"eukaryote":[49],"species,":[50],"providing":[51],"unprecedented":[52],"insight":[53],"into":[54],"evolution":[56],"genes":[58],"gene":[60,71],"families,":[61],"thus":[63],"on":[64,147],"biological":[65,122],"issues.":[66],"Here,":[67],"new":[68],"modules":[69],"annotation,":[72],"further":[73,77,87,137],"BLAST":[74],"search":[75],"algorithms,":[76],"multiple":[78],"alignment":[80],"methods,":[81,90],"adding":[83],"sequences,":[86],"tree":[88],"rooting":[89],"estimation":[92],"rates":[94],"synonymous":[96],"nonsynonymous":[98],"substitutions,":[99],"identification":[102],"positively":[104],"selected":[105],"amino":[106,175],"acid":[107,176],"sites,":[108],"have":[109],"been":[110],"added":[111],"auto-phylo":[113,144,171],"(version":[114],"2),":[115],"a":[116,131,165],"recently":[117],"developed":[118],"software":[119],"address":[121],"problems":[123],"using":[124],"phylogenetic":[125],"inferences.":[126],"Additionally,":[127],"we":[128,168],"present":[129],"auto-phylo-pipeliner,":[130],"graphical":[132],"user":[133],"interface":[134],"application":[135],"facilitates":[138],"creation":[140],"running":[142],"Inferences":[146],"S-RNase":[148,187],"specificity,":[149,188],"are":[150],"critical":[151],"both":[153,191],"cross-based":[154],"breeding":[155],"establishment":[159],"pollination":[161],"requirements.":[162],"Therefore,":[163],"as":[164],"test":[166],"case,":[167],"develop":[169],"an":[170],"pipeline":[172],"identify":[174],"sites":[177],"under":[178],"positive":[179],"selection,":[180],"are,":[182],"principle,":[184],"those":[185],"determining":[186],"starting":[189],"from":[190],"non-annotated":[192],"Prunus":[193],"genomes":[194],"available":[197],"public":[199],"databases.":[200]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}
