{"id":"https://openalex.org/W2463019824","doi":"https://doi.org/10.1093/bioinformatics/btw421","title":"Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods","display_name":"Estimating evolutionary rates using time-structured data: a general comparison of phylogenetic methods","publication_year":2016,"publication_date":"2016-07-13","ids":{"openalex":"https://openalex.org/W2463019824","doi":"https://doi.org/10.1093/bioinformatics/btw421","mag":"2463019824","pmid":"https://pubmed.ncbi.nlm.nih.gov/27412094"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btw421","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw421","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3375/16920428/btw421.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/32/22/3375/16920428/btw421.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5051736895","display_name":"Sebasti\u00e1n Duch\u00eane","orcid":"https://orcid.org/0000-0002-2863-0907"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Sebasti\u00e1n Duch\u00eane","raw_affiliation_strings":["1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia","2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia","3Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia"],"affiliations":[{"raw_affiliation_string":"1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"3Centre for Systems Genomics, University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027424821","display_name":"Jemma L. Geoghegan","orcid":"https://orcid.org/0000-0003-0970-0153"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jemma L. Geoghegan","raw_affiliation_strings":["1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia","2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085736091","display_name":"Edward C. Holmes","orcid":"https://orcid.org/0000-0001-9596-3552"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Edward C. Holmes","raw_affiliation_strings":["1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia","2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"1Marie Bashir Institute of Infectious Diseases and Biosecurity, Charles Perkins Centre, Sydney Medical School, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]},{"raw_affiliation_string":"2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090497511","display_name":"Simon Y. W. Ho","orcid":"https://orcid.org/0000-0002-0361-2307"},"institutions":[{"id":"https://openalex.org/I129604602","display_name":"University of Sydney","ror":"https://ror.org/0384j8v12","country_code":"AU","type":"education","lineage":["https://openalex.org/I129604602"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Simon Y.W. Ho","raw_affiliation_strings":["2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia"],"affiliations":[{"raw_affiliation_string":"2School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia","institution_ids":["https://openalex.org/I129604602"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5051736895"],"corresponding_institution_ids":["https://openalex.org/I129604602","https://openalex.org/I165779595"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.3872,"has_fulltext":false,"cited_by_count":48,"citation_normalized_percentile":{"value":0.9258099,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"32","issue":"22","first_page":"3375","last_page":"3379"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9961000084877014,"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":0.9959999918937683,"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/molecular-clock","display_name":"Molecular clock","score":0.737556517124176},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7013772130012512},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5488404631614685},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.541670024394989},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.5372481346130371},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5159050226211548},{"id":"https://openalex.org/keywords/rate-of-evolution","display_name":"Rate of evolution","score":0.512892484664917},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5107297897338867},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.4833526313304901},{"id":"https://openalex.org/keywords/mutation-rate","display_name":"Mutation rate","score":0.4474199712276459},{"id":"https://openalex.org/keywords/bayes-theorem","display_name":"Bayes' theorem","score":0.4431706666946411},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.4264242351055145},{"id":"https://openalex.org/keywords/variation","display_name":"Variation (astronomy)","score":0.4161333441734314},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4143977165222168},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.35051822662353516},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3336026668548584},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2238161563873291},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.21382221579551697},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.20653387904167175}],"concepts":[{"id":"https://openalex.org/C196662502","wikidata":"https://www.wikidata.org/wiki/Q827541","display_name":"Molecular clock","level":4,"score":0.737556517124176},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7013772130012512},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5488404631614685},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.541670024394989},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5372481346130371},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5159050226211548},{"id":"https://openalex.org/C2777949028","wikidata":"https://www.wikidata.org/wiki/Q25303868","display_name":"Rate of evolution","level":4,"score":0.512892484664917},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5107297897338867},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.4833526313304901},{"id":"https://openalex.org/C98638677","wikidata":"https://www.wikidata.org/wiki/Q2067051","display_name":"Mutation rate","level":3,"score":0.4474199712276459},{"id":"https://openalex.org/C207201462","wikidata":"https://www.wikidata.org/wiki/Q182505","display_name":"Bayes' theorem","level":3,"score":0.4431706666946411},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.4264242351055145},{"id":"https://openalex.org/C2778334786","wikidata":"https://www.wikidata.org/wiki/Q1586270","display_name":"Variation (astronomy)","level":2,"score":0.4161333441734314},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4143977165222168},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.35051822662353516},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3336026668548584},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2238161563873291},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.21382221579551697},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.20653387904167175},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C44870925","wikidata":"https://www.wikidata.org/wiki/Q37547","display_name":"Astrophysics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"D008957","descriptor_name":"Models, Genetic","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":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","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":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":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014780","descriptor_name":"Viruses","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btw421","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw421","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3375/16920428/btw421.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:27412094","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27412094","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":{"id":"doi:10.1093/bioinformatics/btw421","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btw421","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/32/22/3375/16920428/btw421.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":[{"id":"https://openalex.org/F4320320974","display_name":"University of Melbourne","ror":"https://ror.org/01ej9dk98"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2463019824.pdf","grobid_xml":"https://content.openalex.org/works/W2463019824.grobid-xml"},"referenced_works_count":18,"referenced_works":["https://openalex.org/W1903589011","https://openalex.org/W1923320973","https://openalex.org/W1994371781","https://openalex.org/W2000870362","https://openalex.org/W2001750285","https://openalex.org/W2018417559","https://openalex.org/W2029353650","https://openalex.org/W2052694431","https://openalex.org/W2094939159","https://openalex.org/W2111211467","https://openalex.org/W2113439848","https://openalex.org/W2116433762","https://openalex.org/W2120831940","https://openalex.org/W2127398089","https://openalex.org/W2167740275","https://openalex.org/W2274601509","https://openalex.org/W2322358787","https://openalex.org/W4254038116"],"related_works":["https://openalex.org/W2105487208","https://openalex.org/W3191739338","https://openalex.org/W3104823851","https://openalex.org/W2943707377","https://openalex.org/W3044186613","https://openalex.org/W2808314965","https://openalex.org/W2399702402","https://openalex.org/W109727175","https://openalex.org/W763360038","https://openalex.org/W2895729321"],"abstract_inverted_index":{"sduchene@unimelb.edu.au":[0],"or":[1],"garzonsebastian@hotmail.comSupplementary":[2],"information:":[3],"Supplementary":[4],"data":[5],"are":[6],"available":[7],"at":[8],"Bioinformatics":[9],"online.":[10]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":2}],"updated_date":"2026-03-06T13:50:29.536080","created_date":"2025-10-10T00:00:00"}
