{"id":"https://openalex.org/W2904816621","doi":"https://doi.org/10.1093/bioinformatics/bty1019","title":"ModL: exploring and restoring regularity when testing for positive selection","display_name":"ModL: exploring and restoring regularity when testing for positive selection","publication_year":2018,"publication_date":"2018-12-11","ids":{"openalex":"https://openalex.org/W2904816621","doi":"https://doi.org/10.1093/bioinformatics/bty1019","mag":"2904816621","pmid":"https://pubmed.ncbi.nlm.nih.gov/30541063"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty1019","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1019","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5085114753","display_name":"Joseph Mingrone","orcid":null},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Joseph Mingrone","raw_affiliation_strings":["Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada","Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021576212","display_name":"Edward Susko","orcid":"https://orcid.org/0000-0003-1122-8740"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Edward Susko","raw_affiliation_strings":["Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada","Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031897496","display_name":"Joseph P. Bielawski","orcid":"https://orcid.org/0000-0002-1621-1772"},"institutions":[{"id":"https://openalex.org/I129902397","display_name":"Dalhousie University","ror":"https://ror.org/01e6qks80","country_code":"CA","type":"education","lineage":["https://openalex.org/I129902397"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Joseph P Bielawski","raw_affiliation_strings":["Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada","Department of Biology, Dalhousie University, Halifax, NS, Canada","Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Department of Biology, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]},{"raw_affiliation_string":"Department of Mathematics and Statistics, Dalhousie University, Halifax, NS, Canada","institution_ids":["https://openalex.org/I129902397"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5085114753"],"corresponding_institution_ids":["https://openalex.org/I129902397"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5075,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.75161653,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"35","issue":"15","first_page":"2545","last_page":"2554"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.4788999855518341,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.4788999855518341,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.0828000009059906,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.05649999901652336,"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/type-i-and-type-ii-errors","display_name":"Type I and type II errors","score":0.7343934774398804},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.6395968794822693},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6382400989532471},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.5871270298957825},{"id":"https://openalex.org/keywords/statistical-power","display_name":"Statistical power","score":0.5814748406410217},{"id":"https://openalex.org/keywords/null-hypothesis","display_name":"Null hypothesis","score":0.5658313632011414},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.5354511737823486},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.49598249793052673},{"id":"https://openalex.org/keywords/mixing","display_name":"Mixing (physics)","score":0.4688590168952942},{"id":"https://openalex.org/keywords/likelihood-ratio-test","display_name":"Likelihood-ratio test","score":0.4503256380558014},{"id":"https://openalex.org/keywords/power","display_name":"Power (physics)","score":0.44194701313972473},{"id":"https://openalex.org/keywords/model-selection","display_name":"Model selection","score":0.42918357253074646},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4210958480834961},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.42093268036842346},{"id":"https://openalex.org/keywords/chi-square-test","display_name":"Chi-square test","score":0.4194338321685791},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3915879428386688},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.1390540897846222},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.08987748622894287}],"concepts":[{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.7343934774398804},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.6395968794822693},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6382400989532471},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.5871270298957825},{"id":"https://openalex.org/C96608239","wikidata":"https://www.wikidata.org/wiki/Q1199823","display_name":"Statistical power","level":2,"score":0.5814748406410217},{"id":"https://openalex.org/C191988596","wikidata":"https://www.wikidata.org/wiki/Q628374","display_name":"Null hypothesis","level":2,"score":0.5658313632011414},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.5354511737823486},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.49598249793052673},{"id":"https://openalex.org/C138777275","wikidata":"https://www.wikidata.org/wiki/Q6884054","display_name":"Mixing (physics)","level":2,"score":0.4688590168952942},{"id":"https://openalex.org/C9483764","wikidata":"https://www.wikidata.org/wiki/Q585740","display_name":"Likelihood-ratio test","level":2,"score":0.4503256380558014},{"id":"https://openalex.org/C163258240","wikidata":"https://www.wikidata.org/wiki/Q25342","display_name":"Power (physics)","level":2,"score":0.44194701313972473},{"id":"https://openalex.org/C93959086","wikidata":"https://www.wikidata.org/wiki/Q6888345","display_name":"Model selection","level":2,"score":0.42918357253074646},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4210958480834961},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.42093268036842346},{"id":"https://openalex.org/C32809988","wikidata":"https://www.wikidata.org/wiki/Q1071004","display_name":"Chi-square test","level":2,"score":0.4194338321685791},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3915879428386688},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.1390540897846222},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.08987748622894287},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001699","descriptor_name":"Biometry","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":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016009","descriptor_name":"Chi-Square Distribution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty1019","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty1019","pdf_url":null,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30541063","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30541063","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W165370603","https://openalex.org/W1569797516","https://openalex.org/W1628108294","https://openalex.org/W1920973730","https://openalex.org/W1967573895","https://openalex.org/W2016299000","https://openalex.org/W2046076301","https://openalex.org/W2052206449","https://openalex.org/W2057456873","https://openalex.org/W2057538311","https://openalex.org/W2063216803","https://openalex.org/W2101546326","https://openalex.org/W2106068402","https://openalex.org/W2121034387","https://openalex.org/W2125688669","https://openalex.org/W2131713335","https://openalex.org/W2133585817","https://openalex.org/W2140198642","https://openalex.org/W2147307434","https://openalex.org/W2147865566","https://openalex.org/W2150937400","https://openalex.org/W2152076818","https://openalex.org/W2152173558","https://openalex.org/W2160364329","https://openalex.org/W2165578989","https://openalex.org/W2170565120","https://openalex.org/W2476298164","https://openalex.org/W2667453386","https://openalex.org/W2732028845","https://openalex.org/W2810943555","https://openalex.org/W6606786805","https://openalex.org/W6640287769","https://openalex.org/W6741163910"],"related_works":["https://openalex.org/W2897830442","https://openalex.org/W3137029931","https://openalex.org/W2081436506","https://openalex.org/W4313304734","https://openalex.org/W3162828626","https://openalex.org/W2033771870","https://openalex.org/W2145208964","https://openalex.org/W2885070181","https://openalex.org/W2904816621","https://openalex.org/W34221167"],"abstract_inverted_index":{"MOTIVATION:":[0],"Likelihood":[1],"ratio":[2,114,136],"tests":[3,63],"are":[4,16,44,64,212,217,238,252],"commonly":[5,86],"used":[6,87,219],"to":[7,49,121,165,233],"test":[8,77,137],"for":[9,21,180,220],"positive":[10,26],"selection":[11,27],"acting":[12],"on":[13],"proteins.":[14],"They":[15],"usually":[17],"applied":[18],"with":[19,74,193],"thresholds":[20,88],"declaring":[22],"a":[23,30,111,169,221,241],"protein":[24],"under":[25],"determined":[28],"from":[29],"chi-square":[31,35],"or":[32],"mixture":[33,181,215],"of":[34,53,127,146,150,171,183,207,223],"distributions.":[36],"Although":[37],"it":[38],"is":[39,129],"known":[40],"that":[41,60,85,157,177],"such":[42],"distributions":[43,197,203],"not":[45,68,90,130],"strictly":[46],"justified":[47],"due":[48],"the":[50,54,56,61,75,79,125,133,147,151,205,228],"statistical":[51],"irregularity":[52],"problem,":[55],"hope":[57],"has":[58],"been":[59],"resulting":[62],"conservative":[65,92],"and":[66,209,230],"do":[67],"lose":[69],"much":[70],"power":[71],"in":[72,189,225,240],"comparison":[73],"same":[76],"using":[78,110],"unknown,":[80],"correct":[81,140],"threshold.":[82],"We":[83,117],"show":[84,156,176],"need":[89],"yield":[91],"tests,":[93],"but":[94],"instead":[95],"give":[96,118],"larger":[97],"than":[98],"expected":[99],"Type":[100,141,160],"I":[101,142,161],"error":[102,143,162],"rates.":[103],"Statistical":[104],"regularity":[105],"can":[106,186],"be":[107,187],"restored":[108],"by":[109],"modified":[112,134],"likelihood":[113,135],"test.":[115],"RESULTS:":[116],"theoretical":[119],"results":[120],"prove":[122],"that,":[123],"if":[124],"number":[126,206],"sites":[128],"too":[131],"small,":[132],"gives":[138,159],"approximately":[139],"probabilities":[144],"regardless":[145],"parameter":[148,178],"settings":[149,192],"underlying":[152],"null":[153],"hypothesis.":[154],"Simulations":[155],"modification":[158],"rates":[163],"closer":[164],"those":[166],"stated":[167],"without":[168],"loss":[170],"power.":[172],"The":[173],"simulations":[174],"also":[175],"estimation":[179],"models":[182,216],"codon":[184],"evolution":[185],"challenging":[188],"certain":[190],"data-generation":[191],"very":[194],"different":[195],"mixing":[196],"giving":[198],"nearly":[199],"identical":[200],"site":[201],"pattern":[202],"unless":[204],"taxa":[208],"tree":[210],"length":[211],"large.":[213],"Because":[214],"widely":[218],"variety":[222],"problems":[224],"molecular":[226],"evolution,":[227],"challenges":[229],"general":[231],"approaches":[232],"solving":[234],"them":[235],"presented":[236],"here":[237],"applicable":[239],"broader":[242],"context.":[243],"AVAILABILITY":[244],"AND":[245],"IMPLEMENTATION:":[246],"https://github.com/jehops/codeml_modl.":[247],"SUPPLEMENTARY":[248],"INFORMATION:":[249],"Supplementary":[250],"data":[251],"available":[253],"at":[254],"Bioinformatics":[255],"online.":[256]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
