{"id":"https://openalex.org/W2734735318","doi":"https://doi.org/10.1093/bioinformatics/btx229","title":"Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference","display_name":"Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference","publication_year":2017,"publication_date":"2017-04-20","ids":{"openalex":"https://openalex.org/W2734735318","doi":"https://doi.org/10.1093/bioinformatics/btx229","mag":"2734735318","pmid":"https://pubmed.ncbi.nlm.nih.gov/28881964"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i75/25157234/btx229.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i75/25157234/btx229.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024087795","display_name":"Cl\u00e9ment-Marie Train","orcid":null},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Cl\u00e9ment-Marie Train","raw_affiliation_strings":["Center of Integrative Genomics, University of Lausanne, Lausanne, Switzerland","Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Integrative Genomics, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089216831","display_name":"Natasha Glover","orcid":"https://orcid.org/0000-0003-1811-4340"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Natasha M Glover","raw_affiliation_strings":["Center of Integrative Genomics, University of Lausanne, Lausanne, Switzerland","Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Integrative Genomics, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013025384","display_name":"Gast\u00f3n H. Gonnet","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Gaston H Gonnet","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084558956","display_name":"Adrian Altenhoff","orcid":"https://orcid.org/0000-0001-7492-1273"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Adrian M Altenhoff","raw_affiliation_strings":["Department of Computer Science, ETH Zurich, Zurich, Switzerland","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, ETH Zurich, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5050068380","display_name":"Christophe Dessimoz","orcid":"https://orcid.org/0000-0002-2170-853X"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I45129253","display_name":"University College London","ror":"https://ror.org/02jx3x895","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I45129253"]},{"id":"https://openalex.org/I97565354","display_name":"University of Lausanne","ror":"https://ror.org/019whta54","country_code":"CH","type":"education","lineage":["https://openalex.org/I97565354"]}],"countries":["CH","GB"],"is_corresponding":true,"raw_author_name":"Christophe Dessimoz","raw_affiliation_strings":["Center of Integrative Genomics, University of Lausanne, Lausanne, Switzerland","Department of Computer Science, University College London, London, UK","Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland","Department of Genetics, Evolution and Environment, University College London, London, UK","Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center of Integrative Genomics, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Department of Computer Science, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland","institution_ids":["https://openalex.org/I97565354"]},{"raw_affiliation_string":"Department of Genetics, Evolution and Environment, University College London, London, UK","institution_ids":["https://openalex.org/I45129253"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5050068380","https://openalex.org/A5084558956"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088","https://openalex.org/I45129253","https://openalex.org/I97565354"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":11.3652,"has_fulltext":true,"cited_by_count":117,"citation_normalized_percentile":{"value":0.98703219,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"33","issue":"14","first_page":"i75","last_page":"i82"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.6901999711990356,"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"}},"topics":[{"id":"https://openalex.org/T13664","display_name":"Genome Rearrangement Algorithms","score":0.6901999711990356,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.26840001344680786,"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/T12090","display_name":"Language and cultural evolution","score":0.006000000052154064,"subfield":{"id":"https://openalex.org/subfields/3316","display_name":"Cultural Studies"},"field":{"id":"https://openalex.org/fields/33","display_name":"Social Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.7737203240394592},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.7339795231819153},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.6612951755523682},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6073727607727051},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4633026719093323},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.45371872186660767},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.44505277276039124},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4346333146095276},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3092650771141052},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.2935595214366913},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29038822650909424},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.17293301224708557},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11691054701805115}],"concepts":[{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.7737203240394592},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.7339795231819153},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.6612951755523682},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6073727607727051},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4633026719093323},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.45371872186660767},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.44505277276039124},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4346333146095276},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3092650771141052},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.2935595214366913},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29038822650909424},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.17293301224708557},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11691054701805115},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":"Q000235","qualifier_name":"genetics","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":"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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059645","descriptor_name":"Mutation Rate","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":9,"locations":[{"id":"doi:10.1093/bioinformatics/btx229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i75/25157234/btx229.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:28881964","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/28881964","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:5870696","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5870696","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:serval.unil.ch:BIB_7D03376859BC","is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_7D03376859BC","pdf_url":null,"source":{"id":"https://openalex.org/S4306401797","display_name":"SERVAL (Universit\u00e9 de Lausanne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210093590","host_organization_name":"Swiss School of Archaeology in Greece","host_organization_lineage":["https://openalex.org/I4210093590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, vol. 33, no. 14, pp. i75-i82","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/191311","is_oa":false,"landing_page_url":"http://hdl.handle.net/20.500.11850/191311","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics, 33 (14)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:iris.unil.ch:iris/139273","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/139273","pdf_url":"https://iris.unil.ch/bitstreams/d2efc85f-4574-462a-859d-a762f217c2df/download","source":{"id":"https://openalex.org/S7407055444","display_name":"IRIS","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"journal article"},{"id":"pmh:oai:doc.rero.ch:331851","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306400148","display_name":"reroDoc Digital Library","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:eprints.ucl.ac.uk.OAI2:1566831","is_oa":false,"landing_page_url":"https://discovery.ucl.ac.uk/id/eprint/1566831/","pdf_url":null,"source":{"id":"https://openalex.org/S4306400024","display_name":"UCL Discovery (University College London)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I45129253","host_organization_name":"University College London","host_organization_lineage":["https://openalex.org/I45129253"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"   Bioinformatics , 33  (14)   i75-i82.   (2017)      ","raw_type":"Article"},{"id":"doi:10.3929/ethz-b-000191311","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000191311","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx229","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx229","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/33/14/i75/25157234/btx229.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1751534761","display_name":null,"funder_award_id":"150654","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G2921159926","display_name":null,"funder_award_id":"BB/M015009/1","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7411366255","display_name":"Computational Inference of Gene Function in Crop Genomes using Hierarchical Orthologous Groups","funder_award_id":"BB/M015009/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320286","display_name":"University College London","ror":"https://ror.org/02jx3x895"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320331322","display_name":"Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2734735318.pdf"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W1562108164","https://openalex.org/W1972157500","https://openalex.org/W1973810564","https://openalex.org/W1990453950","https://openalex.org/W1995117714","https://openalex.org/W1997093937","https://openalex.org/W1997130867","https://openalex.org/W2004707197","https://openalex.org/W2008856488","https://openalex.org/W2009234149","https://openalex.org/W2012035190","https://openalex.org/W2016681664","https://openalex.org/W2030317329","https://openalex.org/W2044892321","https://openalex.org/W2065375138","https://openalex.org/W2082445660","https://openalex.org/W2087064593","https://openalex.org/W2111414304","https://openalex.org/W2114250447","https://openalex.org/W2132023322","https://openalex.org/W2133218228","https://openalex.org/W2136258184","https://openalex.org/W2159266221","https://openalex.org/W2167188257","https://openalex.org/W2167645766","https://openalex.org/W2316262244","https://openalex.org/W2319188872","https://openalex.org/W4244346553"],"related_works":["https://openalex.org/W2487162673","https://openalex.org/W2378211422","https://openalex.org/W2942366970","https://openalex.org/W2793211469","https://openalex.org/W2949152769","https://openalex.org/W4372354731","https://openalex.org/W2562400057","https://openalex.org/W2745001401","https://openalex.org/W1692008701","https://openalex.org/W4321353415"],"abstract_inverted_index":{"MOTIVATION:":[0],"Accurate":[1],"orthology":[2,64,79,98,149],"inference":[3,65,80],"is":[4,55,173],"a":[5,123],"fundamental":[6],"step":[7,81,100],"in":[8,27,29,43,71,95,113,175],"many":[9],"phylogenetics":[10],"and":[11,42,50,61,91,188,200],"comparative":[12],"analysis.":[13],"Many":[14],"methods":[15],"have":[16],"been":[17],"proposed,":[18],"including":[19],"OMA":[20,73,170,177,196],"(Orthologous":[21],"MAtrix).":[22],"Yet":[23],"substantial":[24,159],"challenges":[25],"remain,":[26],"particular":[28],"coping":[30],"with":[31],"fragmented":[32],"genes":[33,35],"or":[34,207],"evolving":[36,87],"at":[37,88],"different":[38,89],"rates":[39],"after":[40],"duplication,":[41],"scaling":[44],"to":[45,57,82],"large":[46,141],"datasets.":[47,142,164],"With":[48],"more":[49,51,124],"genomes":[52,194],"available,":[53],"it":[54],"necessary":[56],"improve":[58],"the":[59,72,77,96,103,114,144,176,183],"scalability":[60],"robustness":[62],"of":[63,105,116,137],"methods.":[66],"RESULTS:":[67],"We":[68],"present":[69],"improvements":[70],"algorithm:":[74],"(i)":[75],"refining":[76],"pairwise":[78,97,106],"account":[83],"for":[84,127,146],"same-species":[85],"paralogs":[86],"rates,":[90],"(ii)":[92],"minimizing":[93],"errors":[94],"verification":[99],"by":[101],"testing":[102],"consistency":[104],"distance":[107],"estimates,":[108],"which":[109,133],"can":[110,189],"be":[111,190],"problematic":[112],"presence":[115],"fragmentary":[117],"sequences.":[118],"In":[119],"addition":[120],"we":[121,152],"introduce":[122],"scalable":[125],"procedure":[126],"hierarchical":[128],"orthologous":[129],"group":[130],"(HOG)":[131],"clustering,":[132],"are":[134],"several":[135],"orders":[136],"magnitude":[138],"faster":[139],"on":[140,161,192],"Using":[143],"Quest":[145],"Orthologs":[147],"consortium":[148],"benchmark":[150],"service,":[151],"show":[153],"that":[154],"these":[155],"changes":[156],"translate":[157],"into":[158],"improvement":[160],"multiple":[162],"empirical":[163],"AVAILABILITY":[165],"AND":[166],"IMPLEMENTATION:":[167],"This":[168],"new":[169],"2.0":[171,199],"algorithm":[172],"used":[174],"database":[178],"(":[179,202],"http://omabrowser.org":[180],")":[181],"from":[182],"March":[184],"2017":[185],"release":[186],"onwards,":[187],"run":[191],"custom":[193],"using":[195],"standalone":[197],"version":[198],"above":[201],"http://omabrowser.org/standalone":[203],").":[204],"CONTACT:":[205],"christophe.dessimoz@unil.ch":[206],"adrian.altenhoff@inf.ethz.ch.":[208]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":13},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":17},{"year":2021,"cited_by_count":17},{"year":2020,"cited_by_count":16},{"year":2019,"cited_by_count":19},{"year":2018,"cited_by_count":16},{"year":2017,"cited_by_count":1}],"updated_date":"2026-05-22T06:13:13.366637","created_date":"2025-10-10T00:00:00"}
