{"id":"https://openalex.org/W2128841626","doi":"https://doi.org/10.1093/bioinformatics/btm388","title":"AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics","display_name":"AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics","publication_year":2007,"publication_date":"2007-08-30","ids":{"openalex":"https://openalex.org/W2128841626","doi":"https://doi.org/10.1093/bioinformatics/btm388","mag":"2128841626","pmid":"https://pubmed.ncbi.nlm.nih.gov/17766271"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btm388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm388","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/581/49045681/bioinformatics_24_4_581.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/581/49045681/bioinformatics_24_4_581.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049047127","display_name":"Johan A. A. Nylander","orcid":"https://orcid.org/0000-0001-8940-456X"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Johan A.A. Nylander","raw_affiliation_strings":["1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA","institution_ids":["https://openalex.org/I103163165","https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006647644","display_name":"James C. Wilgenbusch","orcid":"https://orcid.org/0000-0001-9464-1578"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"James C. Wilgenbusch","raw_affiliation_strings":["1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA","institution_ids":["https://openalex.org/I103163165","https://openalex.org/I84218800"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008601849","display_name":"Dan L. Warren","orcid":"https://orcid.org/0000-0002-8747-2451"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dan L. Warren","raw_affiliation_strings":["1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA","institution_ids":["https://openalex.org/I103163165","https://openalex.org/I84218800"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073568173","display_name":"David L. Swofford","orcid":"https://orcid.org/0000-0003-0396-1395"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I84218800","display_name":"University of California, Davis","ror":"https://ror.org/05rrcem69","country_code":"US","type":"education","lineage":["https://openalex.org/I84218800"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David L. Swofford","raw_affiliation_strings":["1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 School of Computational Sciences, Florida State University, Tallahassee, Florida 32306 and 2Section of Evolution and Ecology, University of California, Davis, California 95616, USA","institution_ids":["https://openalex.org/I103163165","https://openalex.org/I84218800"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006647644"],"corresponding_institution_ids":["https://openalex.org/I103163165","https://openalex.org/I84218800"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":142.4468,"has_fulltext":true,"cited_by_count":1754,"citation_normalized_percentile":{"value":0.9999175,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"24","issue":"4","first_page":"581","last_page":"583"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.7511000037193298,"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"}},"topics":[{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.7511000037193298,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.17260000109672546,"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/T10421","display_name":"Pleistocene-Era Hominins and Archaeology","score":0.009100000374019146,"subfield":{"id":"https://openalex.org/subfields/3314","display_name":"Anthropology"},"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/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.9270427227020264},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6704243421554565},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.6062812805175781},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.5319697260856628},{"id":"https://openalex.org/keywords/convergence","display_name":"Convergence (economics)","score":0.5147254467010498},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.4928622245788574},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.41333308815956116},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3805505633354187},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35229992866516113},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3432410955429077},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2858582139015198}],"concepts":[{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.9270427227020264},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6704243421554565},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.6062812805175781},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.5319697260856628},{"id":"https://openalex.org/C2777303404","wikidata":"https://www.wikidata.org/wiki/Q759757","display_name":"Convergence (economics)","level":2,"score":0.5147254467010498},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.4928622245788574},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.41333308815956116},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3805505633354187},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35229992866516113},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3432410955429077},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2858582139015198},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C50522688","wikidata":"https://www.wikidata.org/wiki/Q189833","display_name":"Economic growth","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":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btm388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm388","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/581/49045681/bioinformatics_24_4_581.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17766271","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17766271","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:CiteSeerX.psu:10.1.1.132.9027","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.132.9027","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/cgi/reprint/btm388v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btm388","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btm388","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/24/4/581/49045681/bioinformatics_24_4_581.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128841626.pdf","grobid_xml":"https://content.openalex.org/works/W2128841626.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1561594449","https://openalex.org/W1628017834","https://openalex.org/W1994371781","https://openalex.org/W2093223772","https://openalex.org/W2108087670","https://openalex.org/W2146058063","https://openalex.org/W2152886327","https://openalex.org/W2164789250","https://openalex.org/W2331182131","https://openalex.org/W3217097258","https://openalex.org/W4254038116","https://openalex.org/W4285719527","https://openalex.org/W6769428862"],"related_works":["https://openalex.org/W3087071515","https://openalex.org/W4283077537","https://openalex.org/W2999603699","https://openalex.org/W2464065341","https://openalex.org/W2947536360","https://openalex.org/W3086697448","https://openalex.org/W2968689489","https://openalex.org/W4302573481","https://openalex.org/W2372267530","https://openalex.org/W2505308168"],"abstract_inverted_index":{"UNLABELLED:":[0],"A":[1],"key":[2],"element":[3],"to":[4],"a":[5,42,54,62,128,150,169],"successful":[6],"Markov":[7,21],"chain":[8],"Monte":[9],"Carlo":[10],"(MCMC)":[11],"inference":[12],"is":[13,36,157],"the":[14,20,24,31,47,80,93,98,121,136,147,162],"programming":[15],"and":[16,52,74,88,95,167],"run":[17],"performance":[18],"of":[19,27,30,56,58,70,79,97,118,124,127,139,149],"chain.":[22],"However,":[23],"explicit":[25],"use":[26],"quality":[28],"assessments":[29],"MCMC":[32,50,84,152],"simulations-convergence":[33],"diagnostics-in":[34],"phylogenetics":[35],"still":[37],"uncommon.":[38],"Here,":[39],"we":[40],"present":[41],"simple":[43],"tool":[44,101],"that":[45],"uses":[46],"output":[48,81],"from":[49,82],"simulations":[51,85],"visualizes":[53],"number":[55],"properties":[57],"primary":[59],"interest":[60],"in":[61,109],"Bayesian":[63],"phylogenetic":[64,83,151],"analysis,":[65],"such":[66,134],"as":[67,135,159,168],"convergence":[68,105],"rates":[69],"posterior":[71],"split":[72],"probabilities":[73],"branch":[75],"lengths.":[76],"Graphical":[77],"exploration":[78],"gives":[86],"intuitive":[87],"often":[89],"crucial":[90],"information":[91],"on":[92],"success":[94,148],"reliability":[96],"analysis.":[99],"The":[100,155],"presented":[102],"here":[103],"complements":[104],"diagnostics":[106],"already":[107],"available":[108,158],"other":[110,116],"software":[111],"packages":[112],"primarily":[113],"designed":[114],"for":[115,145],"applications":[117],"MCMC.":[119],"Importantly,":[120],"common":[122],"practice":[123],"using":[125],"trace-plots":[126],"single":[129],"parameter":[130],"or":[131],"summary":[132],"statistic,":[133],"likelihood":[137],"score":[138],"sampled":[140],"trees,":[141],"can":[142],"be":[143],"misleading":[144],"assessing":[146],"simulation.":[153],"AVAILABILITY:":[154],"program":[156],"source":[160],"under":[161],"GNU":[163],"General":[164],"Public":[165],"License":[166],"web":[170],"application":[171],"at":[172],"http://ceb.scs.fsu.edu/awty.":[173]},"counts_by_year":[{"year":2026,"cited_by_count":10},{"year":2025,"cited_by_count":32},{"year":2024,"cited_by_count":44},{"year":2023,"cited_by_count":28},{"year":2022,"cited_by_count":49},{"year":2021,"cited_by_count":26},{"year":2020,"cited_by_count":25},{"year":2019,"cited_by_count":43},{"year":2018,"cited_by_count":65},{"year":2017,"cited_by_count":90},{"year":2016,"cited_by_count":115},{"year":2015,"cited_by_count":156},{"year":2014,"cited_by_count":173},{"year":2013,"cited_by_count":168},{"year":2012,"cited_by_count":202}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
