{"id":"https://openalex.org/W1984499481","doi":"https://doi.org/10.3233/978-1-61499-054-3-59","title":"gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution","display_name":"gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution","publication_year":2012,"publication_date":"2012-01-01","ids":{"openalex":"https://openalex.org/W1984499481","doi":"https://doi.org/10.3233/978-1-61499-054-3-59","mag":"1984499481"},"language":"en","primary_location":{"id":"doi:10.3233/978-1-61499-054-3-59","is_oa":false,"landing_page_url":"https://doi.org/10.3233/978-1-61499-054-3-59","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},"type":"book-chapter","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://iris.unil.ch/bitstreams/ec8e4cf8-e363-47d2-8f27-f17518935dcb/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5039131441","display_name":"S\u00e9bastien Moretti","orcid":"https://orcid.org/0000-0003-3947-488X"},"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"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Moretti S&eacute;bastien","raw_affiliation_strings":["Department of Ecology and Evolution, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Ecology and Evolution, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103943631","display_name":"Riccardo Murri","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Murri Riccardo","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077638047","display_name":"Sergio Maffioletti","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Maffioletti Sergio","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077797266","display_name":"Arnold Kuzniar","orcid":"https://orcid.org/0000-0003-1711-7961"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kuzniar Arnold","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063740541","display_name":"Bris\u00e9\u00efs Castella","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Castella Bris&eacute;&iuml;s","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044471833","display_name":"Nicolas Salamin","orcid":"https://orcid.org/0000-0002-3963-4954"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Salamin Nicolas","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054250703","display_name":"Marc Robinson\u2010Rechavi","orcid":"https://orcid.org/0000-0002-3437-3329"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Robinson-Rechavi Marc","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5069082993","display_name":"Heinz Stockinger","orcid":"https://orcid.org/0000-0003-4666-7719"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stockinger Heinz","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5039131441"],"corresponding_institution_ids":["https://openalex.org/I12708293"],"apc_list":null,"apc_paid":null,"fwci":0.9155,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.80004937,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991999864578247,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9991999864578247,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9897000193595886,"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/T11252","display_name":"Evolutionary Game Theory and Cooperation","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/3312","display_name":"Sociology and Political Science"},"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/selection","display_name":"Selection (genetic algorithm)","score":0.6213937401771545},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.5921335220336914},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.47602513432502747},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4186001420021057},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.31906211376190186},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.29522955417633057},{"id":"https://openalex.org/keywords/geography","display_name":"Geography","score":0.2547258138656616}],"concepts":[{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.6213937401771545},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.5921335220336914},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.47602513432502747},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4186001420021057},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.31906211376190186},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.29522955417633057},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.2547258138656616},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3233/978-1-61499-054-3-59","is_oa":false,"landing_page_url":"https://doi.org/10.3233/978-1-61499-054-3-59","pdf_url":null,"source":{"id":"https://openalex.org/S4210179765","display_name":"Studies in health technology and informatics","issn_l":"0926-9630","issn":["0926-9630","1879-8365"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310318577","host_organization_name":"IOS Press","host_organization_lineage":["https://openalex.org/P4310318577"],"host_organization_lineage_names":["IOS Press"],"type":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Studies in Health Technology and Informatics","raw_type":"book-chapter"},{"id":"pmh:oai:serval.unil.ch:BIB_542C5BE6E2B7","is_oa":false,"landing_page_url":"https://serval.unil.ch/notice/serval:BIB_542C5BE6E2B7","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":"HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, vol. 175, pp. 59-68","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:iris.unil.ch:iris/41848","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/41848","pdf_url":"https://iris.unil.ch/bitstreams/ec8e4cf8-e363-47d2-8f27-f17518935dcb/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":"book part"},{"id":"mag:1984499481","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1203.3092","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null}],"best_oa_location":{"id":"pmh:oai:iris.unil.ch:iris/41848","is_oa":true,"landing_page_url":"https://iris.unil.ch/handle/iris/41848","pdf_url":"https://iris.unil.ch/bitstreams/ec8e4cf8-e363-47d2-8f27-f17518935dcb/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":"book part"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.5799999833106995}],"awards":[],"funders":[{"id":"https://openalex.org/F4320323831","display_name":"Universit\u00e9 de Lausanne","ror":"https://ror.org/019whta54"},{"id":"https://openalex.org/F4320331149","display_name":"Board of the Swiss Federal Institutes of Technology","ror":"https://ror.org/01rvn4p91"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1984499481.pdf"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1501643305","https://openalex.org/W1969128841","https://openalex.org/W2003644562","https://openalex.org/W2072328011","https://openalex.org/W2082853993","https://openalex.org/W2089818266","https://openalex.org/W2117306576","https://openalex.org/W2122029391","https://openalex.org/W2132967177","https://openalex.org/W2141269195","https://openalex.org/W2160070700","https://openalex.org/W2163281919","https://openalex.org/W2402402137","https://openalex.org/W2883512297"],"related_works":["https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2061542922"],"abstract_inverted_index":{"One":[0],"of":[1,23],"the":[2,21,47,60],"important":[3],"questions":[4],"in":[5,92],"biological":[6],"evolution":[7],"is":[8,27,85],"to":[9,20,29,45,64,89],"know":[10],"if":[11],"certain":[12],"changes":[13],"along":[14],"protein":[15],"coding":[16],"genes":[17],"have":[18,51],"contributed":[19],"adaptation":[22],"species.":[24],"This":[25],"problem":[26],"known":[28],"be":[30],"biologically":[31],"complex":[32],"and":[33,73,87],"computationally":[34],"very":[35],"expensive.":[36],"It,":[37],"therefore,":[38],"requires":[39],"efficient":[40],"Grid":[41],"or":[42,94],"cluster":[43],"solutions":[44],"overcome":[46],"computational":[48,74],"challenge.":[49],"We":[50],"developed":[52],"a":[53],"Grid-enabled":[54],"tool":[55],"(gcodeml)":[56],"that":[57],"relies":[58],"on":[59,70,79],"PAML":[61],"(codeml)":[62],"package":[63],"help":[65],"analyse":[66],"large":[67],"phylogenetic":[68],"datasets":[69],"both":[71],"Grids":[72],"clusters.":[75],"Although":[76],"we":[77],"report":[78],"results":[80],"for":[81],"gcodeml,":[82],"our":[83],"approach":[84],"applicable":[86],"customisable":[88],"related":[90],"problems":[91],"biology":[93],"other":[95],"scientific":[96],"domains.":[97]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
