{"id":"https://openalex.org/W3116854850","doi":"https://doi.org/10.1093/bioinformatics/btaa820","title":"Using a GTR+\u0393 substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated","display_name":"Using a GTR+\u0393 substitution model for dating sequence divergence when stationarity and time-reversibility assumptions are violated","publication_year":2020,"publication_date":"2020-09-07","ids":{"openalex":"https://openalex.org/W3116854850","doi":"https://doi.org/10.1093/bioinformatics/btaa820","mag":"3116854850","pmid":"https://pubmed.ncbi.nlm.nih.gov/33381826"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa820","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa820","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i884/35337016/btaa820.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/36/Supplement_2/i884/35337016/btaa820.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000997109","display_name":"Jose Barba\u2010Montoya","orcid":"https://orcid.org/0000-0002-1337-8139"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jose Barba-Montoya","raw_affiliation_strings":["Department of Biology, Temple University , Philadelphia, PA 19122, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19122, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016751952","display_name":"Qiqing Tao","orcid":"https://orcid.org/0000-0001-7360-409X"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Qiqing Tao","raw_affiliation_strings":["Department of Biology, Temple University , Philadelphia, PA 19122, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19122, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100680948","display_name":"Sudhir Kumar","orcid":"https://orcid.org/0000-0002-9918-8212"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]},{"id":"https://openalex.org/I185163786","display_name":"King Abdulaziz University","ror":"https://ror.org/02ma4wv74","country_code":"SA","type":"education","lineage":["https://openalex.org/I185163786"]}],"countries":["SA","US"],"is_corresponding":true,"raw_author_name":"Sudhir Kumar","raw_affiliation_strings":["Center for Excellence in Genome Medicine and Research, King Abdulaziz University , Jeddah 21589, Saudi Arabia","Department of Biology, Temple University , Philadelphia, PA 19122, USA","Institute for Genomics and Evolutionary Medicine"],"affiliations":[{"raw_affiliation_string":"Center for Excellence in Genome Medicine and Research, King Abdulaziz University , Jeddah 21589, Saudi Arabia","institution_ids":["https://openalex.org/I185163786"]},{"raw_affiliation_string":"Department of Biology, Temple University , Philadelphia, PA 19122, USA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Institute for Genomics and Evolutionary Medicine","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5100680948"],"corresponding_institution_ids":["https://openalex.org/I185163786","https://openalex.org/I84392919"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.5865,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.68427845,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"36","issue":"Supplement_2","first_page":"i884","last_page":"i894"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10017","display_name":"Geology and Paleoclimatology Research","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1902","display_name":"Atmospheric Science"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10017","display_name":"Geology and Paleoclimatology Research","score":0.9907000064849854,"subfield":{"id":"https://openalex.org/subfields/1902","display_name":"Atmospheric Science"},"field":{"id":"https://openalex.org/fields/19","display_name":"Earth and Planetary Sciences"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10087","display_name":"Archaeology and ancient environmental studies","score":0.9587000012397766,"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"}},{"id":"https://openalex.org/T10012","display_name":"Genetic diversity and population structure","score":0.9258999824523926,"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/substitution","display_name":"Substitution (logic)","score":0.8704860210418701},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.7806710004806519},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.7370407581329346},{"id":"https://openalex.org/keywords/econometrics","display_name":"Econometrics","score":0.5475425124168396},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.42469972372055054},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.39803415536880493},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3242301940917969},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11315500736236572},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10944679379463196},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.06351375579833984},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.06258288025856018}],"concepts":[{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.8704860210418701},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.7806710004806519},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.7370407581329346},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.5475425124168396},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.42469972372055054},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.39803415536880493},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3242301940917969},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11315500736236572},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10944679379463196},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.06351375579833984},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.06258288025856018},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"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":"D005580","descriptor_name":"Fossils","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005580","descriptor_name":"Fossils","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005580","descriptor_name":"Fossils","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa820","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa820","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i884/35337016/btaa820.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:33381826","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33381826","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:7773479","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7773479","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa820","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa820","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_2/i884/35337016/btaa820.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":[{"score":0.5899999737739563,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2466576084","display_name":null,"funder_award_id":"NNX16AJ30G","funder_id":"https://openalex.org/F4320306101","funder_display_name":"National Aeronautics and Space Administration"},{"id":"https://openalex.org/G3303107229","display_name":null,"funder_award_id":"R01GM126567-03","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6762783816","display_name":null,"funder_award_id":"DBI 1356548","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306101","display_name":"National Aeronautics and Space Administration","ror":"https://ror.org/027ka1x80"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3116854850.pdf","grobid_xml":"https://content.openalex.org/works/W3116854850.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W585037855","https://openalex.org/W1487781539","https://openalex.org/W1507241016","https://openalex.org/W1593676244","https://openalex.org/W1838973073","https://openalex.org/W1974477108","https://openalex.org/W1975520815","https://openalex.org/W1983408155","https://openalex.org/W1992566665","https://openalex.org/W1996019265","https://openalex.org/W2009596137","https://openalex.org/W2026551295","https://openalex.org/W2036628186","https://openalex.org/W2051296828","https://openalex.org/W2065461553","https://openalex.org/W2100806401","https://openalex.org/W2110335151","https://openalex.org/W2121552166","https://openalex.org/W2131633033","https://openalex.org/W2136391301","https://openalex.org/W2139771752","https://openalex.org/W2141052558","https://openalex.org/W2144775551","https://openalex.org/W2148960006","https://openalex.org/W2149711625","https://openalex.org/W2157552136","https://openalex.org/W2158482855","https://openalex.org/W2162443218","https://openalex.org/W2168573791","https://openalex.org/W2186750819","https://openalex.org/W2187450834","https://openalex.org/W2590646912","https://openalex.org/W2799524357","https://openalex.org/W2804308203","https://openalex.org/W2915370094","https://openalex.org/W3009411980","https://openalex.org/W4250847479","https://openalex.org/W6681367416","https://openalex.org/W6683885929","https://openalex.org/W6734654818"],"related_works":["https://openalex.org/W2379444625","https://openalex.org/W2393147081","https://openalex.org/W2575869988","https://openalex.org/W4308647020","https://openalex.org/W2370088286","https://openalex.org/W2385568494","https://openalex.org/W2912058948","https://openalex.org/W2588424405","https://openalex.org/W2042068218","https://openalex.org/W2362702465"],"abstract_inverted_index":{"All":[0],"datasets":[1],"are":[2],"deposited":[3],"in":[4],"Figshare:":[5],"https://doi.org/10.6084/m9.figshare.12594638.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-12T07:58:50.170612","created_date":"2025-10-10T00:00:00"}
