{"id":"https://openalex.org/W2162350421","doi":"https://doi.org/10.1093/bioinformatics/btt707","title":"A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data","display_name":"A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data","publication_year":2013,"publication_date":"2013-12-05","ids":{"openalex":"https://openalex.org/W2162350421","doi":"https://doi.org/10.1093/bioinformatics/btt707","mag":"2162350421","pmid":"https://pubmed.ncbi.nlm.nih.gov/24318999"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt707","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt707","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/A5057909697","display_name":"Nicolas Lartillot","orcid":"https://orcid.org/0000-0002-9973-7760"},"institutions":[{"id":"https://openalex.org/I100532134","display_name":"Lyon 1 Universit\u00e9","ror":"https://ror.org/029brtt94","country_code":"FR","type":"education","lineage":["https://openalex.org/I100532134","https://openalex.org/I203339264"]},{"id":"https://openalex.org/I4210135640","display_name":"Laboratoire de Biom\u00e9trie et Biologie Evolutive","ror":"https://ror.org/03skt0t88","country_code":"FR","type":"facility","lineage":["https://openalex.org/I100532134","https://openalex.org/I1294671590","https://openalex.org/I1294671590","https://openalex.org/I1326498283","https://openalex.org/I203339264","https://openalex.org/I4210100596","https://openalex.org/I4210104684","https://openalex.org/I4210107625","https://openalex.org/I4210135640"]},{"id":"https://openalex.org/I70931966","display_name":"Universit\u00e9 de Montr\u00e9al","ror":"https://ror.org/0161xgx34","country_code":"CA","type":"education","lineage":["https://openalex.org/I70931966"]}],"countries":["CA","FR"],"is_corresponding":true,"raw_author_name":"Nicolas Lartillot","raw_affiliation_strings":["1 Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Centre National de la Recherche Scientifique, UMR 5558. Universit\u00e9 Lyon 1, F-69622 Villeurbanne, France and 2Centre Robert-Cedergren pour la Bioinformatique, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Laboratoire de Biom\u00e9trie et Biologie \u00c9volutive, Centre National de la Recherche Scientifique, UMR 5558. Universit\u00e9 Lyon 1, F-69622 Villeurbanne, France and 2Centre Robert-Cedergren pour la Bioinformatique, D\u00e9partement de Biochimie, Universit\u00e9 de Montr\u00e9al, Qu\u00e9bec, Canada","institution_ids":["https://openalex.org/I100532134","https://openalex.org/I4210135640","https://openalex.org/I70931966"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5057909697"],"corresponding_institution_ids":["https://openalex.org/I100532134","https://openalex.org/I4210135640","https://openalex.org/I70931966"],"apc_list":{"value":3989,"currency":"USD","value_usd":3989},"apc_paid":null,"fwci":0.6946,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.70556738,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"30","issue":"4","first_page":"488","last_page":"496"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4291999936103821,"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":0.4291999936103821,"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/T13664","display_name":"Genome Rearrangement Algorithms","score":0.29170000553131104,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.061900001019239426,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6192734241485596},{"id":"https://openalex.org/keywords/trait","display_name":"Trait","score":0.5006659030914307},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.48346003890037537},{"id":"https://openalex.org/keywords/regression","display_name":"Regression","score":0.46641266345977783},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4593944549560547},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.44627389311790466},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.37433964014053345},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.33126235008239746},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.33061641454696655},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.330528199672699},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3084719181060791},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2431786060333252},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.16670438647270203}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6192734241485596},{"id":"https://openalex.org/C106934330","wikidata":"https://www.wikidata.org/wiki/Q1971873","display_name":"Trait","level":2,"score":0.5006659030914307},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.48346003890037537},{"id":"https://openalex.org/C83546350","wikidata":"https://www.wikidata.org/wiki/Q1139051","display_name":"Regression","level":2,"score":0.46641266345977783},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4593944549560547},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.44627389311790466},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.37433964014053345},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.33126235008239746},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.33061641454696655},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.330528199672699},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3084719181060791},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2431786060333252},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.16670438647270203},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001105","descriptor_name":"Archaea","qualifier_ui":"Q000254","qualifier_name":"growth & development","is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001482","descriptor_name":"Base Composition","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":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008390","descriptor_name":"Markov Chains","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012335","descriptor_name":"RNA, Ribosomal","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013696","descriptor_name":"Temperature","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt707","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt707","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:24318999","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24318999","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":"Journal Article"},{"id":"pmh:oai:HAL:hal-02046826v1","is_oa":false,"landing_page_url":"https://univ-lyon1.hal.science/hal-02046826","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics, 2014, 30 (4), pp.488-96. ⟨10.1093/bioinformatics/btt707⟩","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Responsible consumption and production","score":0.46000000834465027,"id":"https://metadata.un.org/sdg/12"},{"display_name":"Life in Land","score":0.44999998807907104,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1514148026","https://openalex.org/W1963617394","https://openalex.org/W1983408155","https://openalex.org/W2013410948","https://openalex.org/W2013907950","https://openalex.org/W2023380041","https://openalex.org/W2061140759","https://openalex.org/W2083114520","https://openalex.org/W2087520649","https://openalex.org/W2102424972","https://openalex.org/W2104398544","https://openalex.org/W2105934661","https://openalex.org/W2107110596","https://openalex.org/W2114525641","https://openalex.org/W2117657845","https://openalex.org/W2117897510","https://openalex.org/W2122512809","https://openalex.org/W2125269856","https://openalex.org/W2127148540","https://openalex.org/W2136437557","https://openalex.org/W2147307434","https://openalex.org/W2149711625","https://openalex.org/W2157009009","https://openalex.org/W2164555431","https://openalex.org/W2178409599","https://openalex.org/W2582743722","https://openalex.org/W6685444281"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"MOTIVATION:":[0],"Correlation":[1],"between":[2],"life":[3],"history":[4,25],"or":[5,14],"ecological":[6],"traits":[7,28],"and":[8,81,105,146,151,172,204],"genomic":[9],"features":[10],"such":[11,36,66],"as":[12,60,67,87],"nucleotide":[13],"amino":[15,205],"acid":[16,206],"composition":[17,199,207],"can":[18],"be":[19,58,134],"used":[20],"for":[21,51,143,224],"reconstructing":[22],"the":[23,27,77,82,93,154,186,189,225],"evolutionary":[24],"of":[26,29,79,156,177,188,191,208,211],"interest":[30,80],"along":[31,92],"phylogenies.":[32],"Thus":[33],"far,":[34],"however,":[35],"ancestral":[37,123],"reconstructions":[38,55,171],"have":[39],"been":[40],"done":[41],"using":[42,197],"simple":[43,181],"linear":[44,182],"regression":[45,64,113,165],"approaches":[46],"that":[47],"do":[48],"not":[49],"account":[50],"phylogenetic":[52,139],"inertia.":[53],"These":[54],"could":[56],"instead":[57],"seen":[59],"a":[61,97,128,138,157,173,209,221],"genuine":[62],"comparative":[63,73,112,164],"problem,":[65,114,142],"formalized":[68],"by":[69],"classical":[70],"generalized":[71,119],"least-square":[72,120],"methods,":[74],"in":[75,153,168,195,200,217],"which":[76,144],"trait":[78,124],"molecular":[83,129],"predictor":[84,130],"are":[85,149],"represented":[86],"correlated":[88],"Brownian":[89],"characters":[90],"coevolving":[91],"phylogeny.":[94],"RESULTS:":[95],"Here,":[96],"Bayesian":[98],"sampler":[99],"is":[100,131,232],"introduced,":[101],"representing":[102],"an":[103],"alternative":[104],"more":[106,169,174],"efficient":[107],"algorithmic":[108],"solution":[109],"to":[110,133,137,185,220],"this":[111],"compared":[115,179],"with":[116,180],"currently":[117],"existing":[118],"approaches.":[121],"Technically,":[122],"reconstruction":[125,187],"based":[126],"on":[127],"shown":[132],"formally":[135],"equivalent":[136],"Kalman":[140],"filter":[141],"backward":[145],"forward":[147],"recursions":[148],"developed":[150],"implemented":[152],"context":[155],"Markov":[158],"chain":[159],"Monte":[160],"Carlo":[161],"sampler.":[162],"The":[163,230],"method":[166],"results":[167],"accurate":[170],"faithful":[175],"representation":[176],"uncertainty,":[178],"regression.":[183],"Application":[184],"evolution":[190],"optimal":[192],"growth":[193],"temperature":[194],"Archaea,":[196],"GC":[198],"ribosomal":[201],"RNA":[202],"stems":[203],"sample":[210],"protein-coding":[212],"genes,":[213],"confirms":[214],"previous":[215],"findings,":[216],"particular,":[218],"pointing":[219],"hyperthermophilic":[222],"ancestor":[223],"kingdom.":[226],"AVAILABILITY":[227],"AND":[228],"IMPLEMENTATION:":[229],"program":[231],"freely":[233],"available":[234],"at":[235],"www.phylobayes.org.":[236]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}