{"id":"https://openalex.org/W2122035212","doi":"https://doi.org/10.1093/bioinformatics/btt340","title":"Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency","display_name":"Bayesian evolutionary model testing in the phylogenomics era: matching model complexity with computational efficiency","publication_year":2013,"publication_date":"2013-06-12","ids":{"openalex":"https://openalex.org/W2122035212","doi":"https://doi.org/10.1093/bioinformatics/btt340","mag":"2122035212","pmid":"https://pubmed.ncbi.nlm.nih.gov/23766415"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1970/49077078/bioinformatics_29_16_1970.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":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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1970/49077078/bioinformatics_29_16_1970.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5056792309","display_name":"Guy Baele","orcid":"https://orcid.org/0000-0002-1915-7732"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":true,"raw_author_name":"Guy Baele","raw_affiliation_strings":["Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium","Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium","institution_ids":["https://openalex.org/I24156275","https://openalex.org/I99464096"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium,","institution_ids":["https://openalex.org/I24156275","https://openalex.org/I99464096"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039280845","display_name":"Philippe Lemey","orcid":"https://orcid.org/0000-0003-2826-5353"},"institutions":[{"id":"https://openalex.org/I24156275","display_name":"Rega Institute for Medical Research","ror":"https://ror.org/03w5j8p12","country_code":"BE","type":"facility","lineage":["https://openalex.org/I24156275"]},{"id":"https://openalex.org/I99464096","display_name":"KU Leuven","ror":"https://ror.org/05f950310","country_code":"BE","type":"education","lineage":["https://openalex.org/I99464096"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Philippe Lemey","raw_affiliation_strings":["Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium","Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium,"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium","institution_ids":["https://openalex.org/I24156275","https://openalex.org/I99464096"]},{"raw_affiliation_string":"Department of Microbiology and Immunology, Rega Institute, KU Leuven, 3000 Leuven, Belgium,","institution_ids":["https://openalex.org/I24156275","https://openalex.org/I99464096"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5056792309"],"corresponding_institution_ids":["https://openalex.org/I24156275","https://openalex.org/I99464096"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.0939,"has_fulltext":false,"cited_by_count":91,"citation_normalized_percentile":{"value":0.94811145,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"29","issue":"16","first_page":"1970","last_page":"1979"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.998199999332428,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.9864000082015991,"subfield":{"id":"https://openalex.org/subfields/1911","display_name":"Paleontology"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6398540735244751},{"id":"https://openalex.org/keywords/estimator","display_name":"Estimator","score":0.5028995871543884},{"id":"https://openalex.org/keywords/phylogenomics","display_name":"Phylogenomics","score":0.49677544832229614},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4403310716152191},{"id":"https://openalex.org/keywords/prior-probability","display_name":"Prior probability","score":0.4307580590248108},{"id":"https://openalex.org/keywords/marginal-likelihood","display_name":"Marginal likelihood","score":0.4140335023403168},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3717638850212097},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.35601624846458435},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3321771025657654},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3207625150680542},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2536468207836151},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.16312584280967712},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.14711269736289978},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.14324596524238586},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12812742590904236}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6398540735244751},{"id":"https://openalex.org/C185429906","wikidata":"https://www.wikidata.org/wiki/Q1130160","display_name":"Estimator","level":2,"score":0.5028995871543884},{"id":"https://openalex.org/C70343354","wikidata":"https://www.wikidata.org/wiki/Q3381973","display_name":"Phylogenomics","level":5,"score":0.49677544832229614},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4403310716152191},{"id":"https://openalex.org/C177769412","wikidata":"https://www.wikidata.org/wiki/Q278090","display_name":"Prior probability","level":3,"score":0.4307580590248108},{"id":"https://openalex.org/C95923904","wikidata":"https://www.wikidata.org/wiki/Q6760420","display_name":"Marginal likelihood","level":3,"score":0.4140335023403168},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3717638850212097},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.35601624846458435},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3321771025657654},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3207625150680542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2536468207836151},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.16312584280967712},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.14711269736289978},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.14324596524238586},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12812742590904236},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.0}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003062","descriptor_name":"Codon","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":"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":"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":"D054629","descriptor_name":"Genome, Mitochondrial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054629","descriptor_name":"Genome, Mitochondrial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054629","descriptor_name":"Genome, Mitochondrial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1970/49077078/bioinformatics_29_16_1970.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23766415","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23766415","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:lirias2repo.kuleuven.be:123456789/417102","is_oa":false,"landing_page_url":"https://lirias.kuleuven.be/bitstream/123456789/417102/1/Baele_Lemey%20-%20Bayesian%20evolutionary%20model%20testing%20in%20the%20phylogenomics%20era%20matching%20model%20complexity%20with%20computational%20efficiency.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306401954","display_name":"Lirias (KU Leuven)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I99464096","host_organization_name":"KU Leuven","host_organization_lineage":["https://openalex.org/I99464096"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, vol. 29 (16), (1970-1979)","raw_type":"info:eu-repo/semantics/publishedVersion"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt340","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt340","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/1970/49077078/bioinformatics_29_16_1970.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2122035212.pdf","grobid_xml":"https://content.openalex.org/works/W2122035212.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W611834007","https://openalex.org/W1525734744","https://openalex.org/W1579352620","https://openalex.org/W1593676244","https://openalex.org/W1638753340","https://openalex.org/W1881807356","https://openalex.org/W1920973730","https://openalex.org/W1977862457","https://openalex.org/W1987423081","https://openalex.org/W2004514718","https://openalex.org/W2009596137","https://openalex.org/W2030962485","https://openalex.org/W2035326297","https://openalex.org/W2051296828","https://openalex.org/W2051500083","https://openalex.org/W2056568233","https://openalex.org/W2079213755","https://openalex.org/W2094939159","https://openalex.org/W2098538101","https://openalex.org/W2098998255","https://openalex.org/W2103116723","https://openalex.org/W2108087670","https://openalex.org/W2116111392","https://openalex.org/W2118048521","https://openalex.org/W2118224447","https://openalex.org/W2123696055","https://openalex.org/W2126606792","https://openalex.org/W2127320825","https://openalex.org/W2130362098","https://openalex.org/W2133585817","https://openalex.org/W2136485386","https://openalex.org/W2136577221","https://openalex.org/W2140099453","https://openalex.org/W2145992798","https://openalex.org/W2146602601","https://openalex.org/W2147660889","https://openalex.org/W2150920748","https://openalex.org/W2158128575","https://openalex.org/W2160634817","https://openalex.org/W2161384597","https://openalex.org/W2162350655","https://openalex.org/W2164887069","https://openalex.org/W2169981472","https://openalex.org/W2171142493","https://openalex.org/W6639376086","https://openalex.org/W6640287769"],"related_works":["https://openalex.org/W590826047","https://openalex.org/W2135187896","https://openalex.org/W3125442035","https://openalex.org/W2184215046","https://openalex.org/W2134898590","https://openalex.org/W3133492393","https://openalex.org/W2885043159","https://openalex.org/W3084136375","https://openalex.org/W4306878334","https://openalex.org/W4225820491"],"abstract_inverted_index":{"We":[0,62,86],"show":[1],"that":[2,88],"a":[3,12,32,69],"full":[4],"codon":[5,34,51,60],"model":[6],"best":[7],"describes":[8],"the":[9,43,64,75,105],"features":[10],"of":[11,18,47,66,71,92],"whole":[13],"mitochondrial":[14],"genome":[15],"dataset,":[16],"consisting":[17],"12":[19],"protein-coding":[20],"genes,":[21],"but":[22],"only":[23],"when":[24,37],"each":[25],"gene":[26],"is":[27],"allowed":[28],"to":[29,96],"evolve":[30],"under":[31],"separate":[33],"model.":[35],"However,":[36],"using":[38,74],"hierarchical":[39],"prior":[40],"specification":[41],"for":[42,78],"partition-specific":[44],"parameters":[45],"instead":[46],"independent":[48],"diffuse":[49],"priors,":[50],"position":[52],"partitioned":[53],"nucleotide":[54],"models":[55,73,94],"can":[56],"still":[57],"outperform":[58],"standard":[59],"models.":[61],"demonstrate":[63],"feasibility":[65],"fitting":[67],"such":[68,93],"combination":[70,81],"complex":[72],"BEAGLE":[76],"library":[77],"BEAST":[79],"in":[80],"with":[82],"recent":[83],"graphics":[84],"cards.":[85],"argue":[87],"development":[89],"and":[90,108],"use":[91],"needs":[95],"be":[97],"accompanied":[98],"by":[99],"state-of-the-art":[100],"marginal":[101],"likelihood":[102],"estimators":[103,112],"because":[104],"more":[106],"traditional":[107],"computationally":[109],"less":[110],"demanding":[111],"do":[113],"not":[114],"offer":[115],"adequate":[116],"accuracy.":[117]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":11},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":13},{"year":2017,"cited_by_count":12},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":8},{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}