{"id":"https://openalex.org/W2101180168","doi":"https://doi.org/10.1093/bioinformatics/btn607","title":"Phylogenetic inference under recombination using Bayesian stochastic topology selection","display_name":"Phylogenetic inference under recombination using Bayesian stochastic topology selection","publication_year":2008,"publication_date":"2008-11-20","ids":{"openalex":"https://openalex.org/W2101180168","doi":"https://doi.org/10.1093/bioinformatics/btn607","mag":"2101180168","pmid":"https://pubmed.ncbi.nlm.nih.gov/19028720"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btn607","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn607","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":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2639012","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5013489448","display_name":"Alex Webb","orcid":"https://orcid.org/0000-0003-0261-4375"},"institutions":[{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Alex Webb","raw_affiliation_strings":["1 Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG and 2MRC Harwell, Oxfordshire, OX11 0RD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG and 2MRC Harwell, Oxfordshire, OX11 0RD, UK","institution_ids":["https://openalex.org/I4210086857"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030731998","display_name":"John M. Hancock","orcid":"https://orcid.org/0000-0003-2991-2217"},"institutions":[{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"John M. Hancock","raw_affiliation_strings":["1 Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG and 2MRC Harwell, Oxfordshire, OX11 0RD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG and 2MRC Harwell, Oxfordshire, OX11 0RD, UK","institution_ids":["https://openalex.org/I4210086857"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100649922","display_name":"Chris Holmes","orcid":"https://orcid.org/0000-0002-6667-4943"},"institutions":[{"id":"https://openalex.org/I4210086857","display_name":"Mary Lyon Centre at MRC Harwell","ror":"https://ror.org/0001h1y25","country_code":"GB","type":"facility","lineage":["https://openalex.org/I4210086857","https://openalex.org/I4210087105","https://openalex.org/I90344618"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Chris C. Holmes","raw_affiliation_strings":["1 Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG and 2MRC Harwell, Oxfordshire, OX11 0RD, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Statistics, 1 South Parks Road, Oxford, OX1 3TG and 2MRC Harwell, Oxfordshire, OX11 0RD, UK","institution_ids":["https://openalex.org/I4210086857"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210086857"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.4041,"has_fulltext":false,"cited_by_count":23,"citation_normalized_percentile":{"value":0.80764519,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"25","issue":"2","first_page":"197","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.8156999945640564,"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":0.8156999945640564,"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":0.11599999666213989,"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":0.02459999918937683,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6341719031333923},{"id":"https://openalex.org/keywords/hidden-markov-model","display_name":"Hidden Markov model","score":0.5581788420677185},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5076035261154175},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5075145959854126},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5048485398292542},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.49142634868621826},{"id":"https://openalex.org/keywords/spurious-relationship","display_name":"Spurious relationship","score":0.46055424213409424},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.45663362741470337},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4425833225250244},{"id":"https://openalex.org/keywords/recombination","display_name":"Recombination","score":0.4275173842906952},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3727112114429474},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.34069597721099854},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3289789855480194},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.2898257076740265},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2642669081687927},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.20442825555801392},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.18339726328849792},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.12661665678024292}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6341719031333923},{"id":"https://openalex.org/C23224414","wikidata":"https://www.wikidata.org/wiki/Q176769","display_name":"Hidden Markov model","level":2,"score":0.5581788420677185},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5076035261154175},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5075145959854126},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5048485398292542},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.49142634868621826},{"id":"https://openalex.org/C97256817","wikidata":"https://www.wikidata.org/wiki/Q1462316","display_name":"Spurious relationship","level":2,"score":0.46055424213409424},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.45663362741470337},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4425833225250244},{"id":"https://openalex.org/C156695909","wikidata":"https://www.wikidata.org/wiki/Q3373825","display_name":"Recombination","level":3,"score":0.4275173842906952},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3727112114429474},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.34069597721099854},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3289789855480194},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2898257076740265},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2642669081687927},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.20442825555801392},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.18339726328849792},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.12661665678024292}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"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":"D008390","descriptor_name":"Markov Chains","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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011995","descriptor_name":"Recombination, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btn607","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btn607","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:19028720","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19028720","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:ora.ox.ac.uk:uuid:54b1583f-95e6-489a-a5f7-52e49088cbf5","is_oa":false,"landing_page_url":"https://ora.ox.ac.uk/objects/uuid:54b1583f-95e6-489a-a5f7-52e49088cbf5","pdf_url":null,"source":{"id":"https://openalex.org/S4306402636","display_name":"Oxford University Research Archive (ORA) (University of Oxford)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I40120149","host_organization_name":"University of Oxford","host_organization_lineage":["https://openalex.org/I40120149"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Symplectic Elements at Oxford","raw_type":"Journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2639012","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2639012","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"pmh:oai:pubmedcentral.nih.gov:2639012","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2639012","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":32,"referenced_works":["https://openalex.org/W1880845650","https://openalex.org/W1971836750","https://openalex.org/W1974402964","https://openalex.org/W1977169047","https://openalex.org/W2007358765","https://openalex.org/W2009596137","https://openalex.org/W2042789248","https://openalex.org/W2048335804","https://openalex.org/W2053117659","https://openalex.org/W2069084739","https://openalex.org/W2073609790","https://openalex.org/W2084416457","https://openalex.org/W2102424972","https://openalex.org/W2106101113","https://openalex.org/W2106706098","https://openalex.org/W2108184101","https://openalex.org/W2121278300","https://openalex.org/W2125359798","https://openalex.org/W2125838338","https://openalex.org/W2129588663","https://openalex.org/W2130416410","https://openalex.org/W2145177374","https://openalex.org/W2150297520","https://openalex.org/W2150855003","https://openalex.org/W2172142645","https://openalex.org/W3008617006","https://openalex.org/W3199943451","https://openalex.org/W4233815609","https://openalex.org/W6667753459","https://openalex.org/W6671391044","https://openalex.org/W6678804063","https://openalex.org/W6682464342"],"related_works":["https://openalex.org/W2162899405","https://openalex.org/W3113091479","https://openalex.org/W941090075","https://openalex.org/W2044987316","https://openalex.org/W2237480245","https://openalex.org/W3134374554","https://openalex.org/W2519167559","https://openalex.org/W2075065631","https://openalex.org/W4288358396","https://openalex.org/W4311248832"],"abstract_inverted_index":{"MOTIVATION:":[0],"Conventional":[1],"phylogenetic":[2,51],"analysis":[3],"for":[4,38,78],"characterizing":[5],"the":[6,23,57,81,86,91,100,143,158,175],"relatedness":[7,92],"between":[8,17,196],"taxa":[9],"typically":[10],"assumes":[11],"that":[12,189],"a":[13,35,49,62,94,113,161],"single":[14],"relationship":[15],"exists":[16],"species":[18],"at":[19,93],"every":[20],"site":[21],"along":[22,56,72],"genome.":[24,58],"This":[25],"assumption":[26],"fails":[27],"to":[28,44,67,85,129,157,169,194,209],"take":[29],"into":[30],"account":[31],"recombination":[32,173,205],"which":[33,53],"is":[34],"fundamental":[36],"process":[37],"generating":[39],"diversity":[40],"and":[41,106,115,155,199],"can":[42],"lead":[43],"spurious":[45],"results.":[46],"Recombination":[47],"induces":[48],"localized":[50],"structure":[52,108,126],"may":[54],"vary":[55],"Here,":[59],"we":[60],"generalize":[61],"hidden":[63,82,103],"Markov":[64,119],"model":[65],"(HMM)":[66],"infer":[68],"changes":[69],"in":[70,137,174,201],"phylogeny":[71,202],"multiple":[73],"sequence":[74],"alignments":[75],"while":[76],"accounting":[77],"rate":[79,197],"heterogeneity;":[80],"states":[83,104],"refer":[84],"unobserved":[87],"phylogenic":[88],"topology":[89],"underlying":[90],"genomic":[95],"location.":[96],"The":[97,124],"dimensionality":[98],"of":[99,102,160,172,177],"number":[101],"(topologies)":[105],"their":[107],"are":[109,116],"random":[110],"(not":[111],"known":[112],"priori)":[114],"sampled":[117],"using":[118],"chain":[120],"Monte":[121],"Carlo":[122],"algorithms.":[123],"HMM":[125],"allows":[127,192],"us":[128,193],"analytically":[130],"integrate":[131],"out":[132],"over":[133],"all":[134,142],"possible":[135],"changepoints":[136],"topologies":[138],"as":[139,141,166,168],"well":[140,167],"unknown":[144],"branch":[145],"lengths.":[146],"RESULTS:":[147],"We":[148],"demonstrate":[149],"our":[150,190],"approach":[151],"on":[152],"simulated":[153],"data":[154],"also":[156],"genome":[159],"suspected":[162],"HIV":[163],"recombinant":[164],"strain":[165],"an":[170],"investigation":[171],"sequences":[176],"15":[178],"laboratory":[179],"mouse":[180],"strains":[181],"sequenced":[182],"by":[183,204],"Perlegen":[184],"Sciences.":[185],"Our":[186],"findings":[187],"indicate":[188],"method":[191],"distinguish":[195],"heterogeneity":[198],"variation":[200],"caused":[203],"without":[206],"being":[207],"restricted":[208],"4-taxa":[210],"data.":[211]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"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":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}