{"id":"https://openalex.org/W2034530888","doi":"https://doi.org/10.1186/1748-7188-8-26","title":"Recursive algorithms for phylogenetic tree counting","display_name":"Recursive algorithms for phylogenetic tree counting","publication_year":2013,"publication_date":"2013-10-28","ids":{"openalex":"https://openalex.org/W2034530888","doi":"https://doi.org/10.1186/1748-7188-8-26","mag":"2034530888","pmid":"https://pubmed.ncbi.nlm.nih.gov/24164709"},"language":"en","primary_location":{"id":"doi:10.1186/1748-7188-8-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-26","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-26","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-26","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040438451","display_name":"Alexandra Gavryushkina","orcid":"https://orcid.org/0000-0002-1885-1108"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Alexandra Gavryushkina","raw_affiliation_strings":["Department of Computer Science, The University of Auckland, Auckland, New Zealand. sasha.gavryushkina@auckland.ac.nz","Department of Computer Science, The University of Auckland, Auckland, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Auckland, Auckland, New Zealand. sasha.gavryushkina@auckland.ac.nz","institution_ids":["https://openalex.org/I154130895"]},{"raw_affiliation_string":"Department of Computer Science, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051299223","display_name":"David Welch","orcid":"https://orcid.org/0000-0002-7066-2830"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"David Welch","raw_affiliation_strings":["Department of Computer Science, The University of Auckland, Auckland, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079724732","display_name":"Alexei J. Drummond","orcid":"https://orcid.org/0000-0003-4454-2576"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]},{"id":"https://openalex.org/I4210117681","display_name":"Allan Wilson Centre","ror":"https://ror.org/02gbgwz87","country_code":"NZ","type":"facility","lineage":["https://openalex.org/I4210117681","https://openalex.org/I51158804"]}],"countries":["NZ"],"is_corresponding":false,"raw_author_name":"Alexei J Drummond","raw_affiliation_strings":["Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand","Department of Computer Science, The University of Auckland, Auckland, New Zealand"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895","https://openalex.org/I4210117681"]},{"raw_affiliation_string":"Department of Computer Science, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5040438451"],"corresponding_institution_ids":["https://openalex.org/I154130895"],"apc_list":{"value":2490,"currency":"USD","value_usd":2490},"apc_paid":{"value":2490,"currency":"USD","value_usd":2490},"fwci":5.5032,"has_fulltext":true,"cited_by_count":14,"citation_normalized_percentile":{"value":0.94705084,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"8","issue":"1","first_page":"26","last_page":"26"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11354","display_name":"Evolution and Paleontology Studies","score":0.24729999899864197,"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":0.24729999899864197,"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/T10421","display_name":"Pleistocene-Era Hominins and Archaeology","score":0.19850000739097595,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13269999623298645,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6720618605613708},{"id":"https://openalex.org/keywords/interval-tree","display_name":"Interval tree","score":0.5872407555580139},{"id":"https://openalex.org/keywords/k-ary-tree","display_name":"K-ary tree","score":0.5714128017425537},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.5446245074272156},{"id":"https://openalex.org/keywords/tree-rearrangement","display_name":"Tree rearrangement","score":0.5284659266471863},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5124233365058899},{"id":"https://openalex.org/keywords/time-complexity","display_name":"Time complexity","score":0.5042513608932495},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.4932522177696228},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4808979034423828},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4697330892086029},{"id":"https://openalex.org/keywords/divergence","display_name":"Divergence (linguistics)","score":0.44482311606407166},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.4404464662075043},{"id":"https://openalex.org/keywords/search-tree","display_name":"Search tree","score":0.4312141239643097},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4247586727142334},{"id":"https://openalex.org/keywords/tree-structure","display_name":"Tree structure","score":0.36454886198043823},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.33172833919525146},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.24271604418754578},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.18427357077598572},{"id":"https://openalex.org/keywords/binary-tree","display_name":"Binary tree","score":0.1392703354358673},{"id":"https://openalex.org/keywords/search-algorithm","display_name":"Search algorithm","score":0.10879552364349365}],"concepts":[{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6720618605613708},{"id":"https://openalex.org/C84927040","wikidata":"https://www.wikidata.org/wiki/Q6057306","display_name":"Interval tree","level":4,"score":0.5872407555580139},{"id":"https://openalex.org/C100560664","wikidata":"https://www.wikidata.org/wiki/Q3608019","display_name":"K-ary tree","level":4,"score":0.5714128017425537},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.5446245074272156},{"id":"https://openalex.org/C53208351","wikidata":"https://www.wikidata.org/wiki/Q7837630","display_name":"Tree rearrangement","level":4,"score":0.5284659266471863},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5124233365058899},{"id":"https://openalex.org/C311688","wikidata":"https://www.wikidata.org/wiki/Q2393193","display_name":"Time complexity","level":2,"score":0.5042513608932495},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.4932522177696228},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4808979034423828},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4697330892086029},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.44482311606407166},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.4404464662075043},{"id":"https://openalex.org/C207024777","wikidata":"https://www.wikidata.org/wiki/Q621673","display_name":"Search tree","level":3,"score":0.4312141239643097},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4247586727142334},{"id":"https://openalex.org/C163797641","wikidata":"https://www.wikidata.org/wiki/Q2067937","display_name":"Tree structure","level":3,"score":0.36454886198043823},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.33172833919525146},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.24271604418754578},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.18427357077598572},{"id":"https://openalex.org/C197855036","wikidata":"https://www.wikidata.org/wiki/Q380172","display_name":"Binary tree","level":2,"score":0.1392703354358673},{"id":"https://openalex.org/C125583679","wikidata":"https://www.wikidata.org/wiki/Q755673","display_name":"Search algorithm","level":2,"score":0.10879552364349365},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1748-7188-8-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-26","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-26","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:24164709","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24164709","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":"Algorithms for molecular biology : AMB","raw_type":"Journal Article"},{"id":"pmh:oai:europepmc.org:2819538","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3829674","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/130454","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/130454","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Algorithms for Molecular Biology, 8","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.3929/ethz-b-000130454","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000130454","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.1186/1748-7188-8-26","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1748-7188-8-26","pdf_url":"https://almob.biomedcentral.com/counter/pdf/10.1186/1748-7188-8-26","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320320006","display_name":"Royal Society","ror":"https://ror.org/03wnrjx87"},{"id":"https://openalex.org/F4320320774","display_name":"Royal Society Te Ap\u0101rangi","ror":"https://ror.org/04tajb587"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2034530888.pdf","grobid_xml":"https://content.openalex.org/works/W2034530888.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W107021117","https://openalex.org/W603816015","https://openalex.org/W1983002447","https://openalex.org/W2007593785","https://openalex.org/W2027600585","https://openalex.org/W2036628186","https://openalex.org/W2043887813","https://openalex.org/W2122980269","https://openalex.org/W2125241803","https://openalex.org/W2167740275","https://openalex.org/W2328115122","https://openalex.org/W4233815609","https://openalex.org/W4388212639"],"related_works":["https://openalex.org/W2227684440","https://openalex.org/W2321133989","https://openalex.org/W2359095153","https://openalex.org/W1559350420","https://openalex.org/W2951172905","https://openalex.org/W2156833871","https://openalex.org/W2083751087","https://openalex.org/W2566588687","https://openalex.org/W1521720839","https://openalex.org/W2150988524"],"abstract_inverted_index":{"BACKGROUND:":[0],"In":[1],"Bayesian":[2,191],"phylogenetic":[3],"inference":[4,68,196],"we":[5],"are":[6,75,200,204],"interested":[7],"in":[8,19,66,99],"distributions":[9],"over":[10],"a":[11,20,110,129,136,154,160,169],"space":[12,22,29],"of":[13,17,27,86,102,107,109,117,128,143,157,177],"trees.":[14],"The":[15],"number":[16,85,101,116,142,176],"trees":[18,87,147,179],"tree":[21,55,72,79,112,163],"is":[23,31,58,64,88,97,119],"an":[24,94],"important":[25],"characteristic":[26],"the":[28,42,54,67,71,84,100,115,141,175],"and":[30,46,82,167],"useful":[32],"for":[33,105,139,173,190],"specifying":[34],"prior":[35,48],"distributions.":[36],"When":[37],"all":[38],"samples":[39],"come":[40],"from":[41],"same":[43],"time":[44,171],"point":[45],"no":[47],"information":[49],"available":[50],"on":[51,148,180],"divergence":[52],"times,":[53],"counting":[56,83,106,126,140,174],"problem":[57],"easy.":[59],"However,":[60],"when":[61,197],"fossil":[62,198],"evidence":[63],"used":[65],"to":[69,125],"constrain":[70],"or":[73,202],"data":[74,199,203],"sampled":[76,103,150,165,182],"serially,":[77],"new":[78,155],"spaces":[80],"arise":[81],"more":[89],"difficult.":[90],"RESULTS:":[91],"We":[92,121,134,152],"describe":[93,135,168],"algorithm":[95,124,138,172],"that":[96,114],"polynomial":[98],"individuals":[104],"resolutions":[108,127],"constraint":[111,132],"assuming":[113],"constraints":[118],"fixed.":[120],"generalise":[122],"this":[123],"fully":[130,145,161],"ranked":[131,146,162],"tree.":[133],"quadratic":[137],"possible":[144],"n":[149,181],"individuals.":[151,183],"introduce":[153],"type":[156],"tree,":[158],"called":[159],"with":[164],"ancestors,":[166],"cubic":[170],"such":[178],"CONCLUSIONS:":[184],"These":[185],"algorithms":[186],"should":[187],"be":[188],"employed":[189],"Markov":[192],"chain":[193],"Monte":[194],"Carlo":[195],"included":[201],"serially":[205],"sampled.":[206]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":4}],"updated_date":"2026-08-21T09:56:20.448147","created_date":"2025-10-10T00:00:00"}