{"id":"https://openalex.org/W118440964","doi":null,"title":"Inferring large phylogenies: The big tree problem","display_name":"Inferring large phylogenies: The big tree problem","publication_year":2006,"publication_date":"2006-01-01","ids":{"openalex":"https://openalex.org/W118440964","mag":"118440964"},"language":"en","primary_location":{"id":"pmh:oai:summit.sfu.ca:3807","doi":null,"is_oa":false,"landing_page_url":"http://summit.sfu.ca/item/3807","pdf_url":null,"source":{"id":"https://openalex.org/S4306400490","display_name":"Summit (Simon Fraser University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I18014758","host_organization_name":"Simon Fraser University","host_organization_lineage":["https://openalex.org/I18014758"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/3807/etd2460.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053461897","display_name":"Rutger Aldo Vos","orcid":"https://orcid.org/0000-0001-9254-7318","observed_orcids":["https://orcid.org/0000-0001-9254-7318"]},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Rutger Vos","raw_affiliation_strings":["Simon Fraser University"],"raw_orcid":"https://orcid.org/0000-0001-9254-7318","affiliations":[{"raw_affiliation_string":"Simon Fraser University","institution_ids":["https://openalex.org/I18014758"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5053461897"],"corresponding_institution_ids":["https://openalex.org/I18014758"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":17,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9878000020980835,"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":0.9878000020980835,"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/T11354","display_name":"Evolution and Paleontology Studies","score":0.0034000000450760126,"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/T10012","display_name":"Genetic diversity and population structure","score":0.00139999995008111,"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-reconstruction","display_name":"phylogenetic inference","score":0.8069999814033508},{"id":"https://openalex.org/keywords/large-phylogenies","display_name":"large phylogenies","score":0.8610000014305115},{"id":"https://openalex.org/keywords/supertree","display_name":"supertree","score":0.7570000290870667},{"id":"https://openalex.org/keywords/bayesian-phylogenetics","display_name":"Bayesian phylogenetics","score":0.9890000224113464},{"id":"https://openalex.org/keywords/primate-phylogeny","display_name":"primate phylogeny","score":0.7889999747276306},{"id":"https://openalex.org/keywords/divergence-time-estimation","display_name":"divergence time estimation","score":0.8820000290870667},{"id":"https://openalex.org/keywords/clock-genes","display_name":"clock genes","score":0.6769999861717224}],"concepts":[{"id":"https://openalex.org/C55919133","wikidata":"https://www.wikidata.org/wiki/Q7644297","display_name":"Supertree","level":4,"score":0.8531936407089233},{"id":"https://openalex.org/C104343652","wikidata":"https://www.wikidata.org/wiki/Q631768","display_name":"Cladogenesis","level":5,"score":0.7449132204055786},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5993866920471191},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4874889850616455},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.48026227951049805},{"id":"https://openalex.org/C207390915","wikidata":"https://www.wikidata.org/wiki/Q1230525","display_name":"Divergence (linguistics)","level":2,"score":0.45287996530532837},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4436851739883423},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4312344789505005},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4122138023376465},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3801853060722351},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.32473501563072205},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.29250943660736084},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.27752214670181274},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.18745481967926025},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10657313466072083},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"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/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:summit.sfu.ca:3807","doi":null,"is_oa":false,"landing_page_url":"http://summit.sfu.ca/item/3807","pdf_url":null,"source":{"id":"https://openalex.org/S4306400490","display_name":"Summit (Simon Fraser University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I18014758","host_organization_name":"Simon Fraser University","host_organization_lineage":["https://openalex.org/I18014758"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Thesis"},{"id":"pmh:oai:summit.sfu.ca:node-3807","doi":null,"is_oa":true,"landing_page_url":"https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/3807/etd2460.pdf","pdf_url":"https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/3807/etd2460.pdf","source":{"id":"https://openalex.org/S4306400490","display_name":"Summit (Simon Fraser University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I18014758","host_organization_name":"Simon Fraser University","host_organization_lineage":["https://openalex.org/I18014758"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"mag:118440964","doi":null,"is_oa":false,"landing_page_url":"https://www.sfu.ca/~amooers/papers/Vos_Dissertation06_chV.pdf","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:summit.sfu.ca:node-3807","doi":null,"is_oa":true,"landing_page_url":"https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/3807/etd2460.pdf","pdf_url":"https://summit.sfu.ca/_flysystem/fedora/sfu_migrate/3807/etd2460.pdf","source":{"id":"https://openalex.org/S4306400490","display_name":"Summit (Simon Fraser University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I18014758","host_organization_name":"Simon Fraser University","host_organization_lineage":["https://openalex.org/I18014758"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320322551","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28"},{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W118440964.pdf","grobid_xml":"https://content.openalex.org/works/W118440964.grobid-xml"},"referenced_works_count":60,"referenced_works":["https://openalex.org/W99397962","https://openalex.org/W117570235","https://openalex.org/W138443391","https://openalex.org/W154881315","https://openalex.org/W1526568321","https://openalex.org/W1541429054","https://openalex.org/W1550929454","https://openalex.org/W1563401818","https://openalex.org/W1594381616","https://openalex.org/W1965007097","https://openalex.org/W1967209299","https://openalex.org/W1968870114","https://openalex.org/W1974246480","https://openalex.org/W1974490559","https://openalex.org/W1977513731","https://openalex.org/W1981529687","https://openalex.org/W1990263013","https://openalex.org/W1991966221","https://openalex.org/W1994371781","https://openalex.org/W2000791515","https://openalex.org/W2006444758","https://openalex.org/W2007835754","https://openalex.org/W2011158918","https://openalex.org/W2011187596","https://openalex.org/W2029353325","https://openalex.org/W2033854905","https://openalex.org/W2039049486","https://openalex.org/W2039644197","https://openalex.org/W2040287264","https://openalex.org/W2055731627","https://openalex.org/W2058993504","https://openalex.org/W2066002165","https://openalex.org/W2066494521","https://openalex.org/W2071248635","https://openalex.org/W2071301830","https://openalex.org/W2075358204","https://openalex.org/W2079157986","https://openalex.org/W2081030047","https://openalex.org/W2081113657","https://openalex.org/W2082928585","https://openalex.org/W2088512249","https://openalex.org/W2093266174","https://openalex.org/W2094277888","https://openalex.org/W2100531129","https://openalex.org/W2123019209","https://openalex.org/W2124478858","https://openalex.org/W2126763909","https://openalex.org/W2132733863","https://openalex.org/W2139062799","https://openalex.org/W2145608399","https://openalex.org/W2146243941","https://openalex.org/W2152038093","https://openalex.org/W2154552181","https://openalex.org/W2158326671","https://openalex.org/W2162703948","https://openalex.org/W2163357043","https://openalex.org/W2163721176","https://openalex.org/W2473726166","https://openalex.org/W2795938539","https://openalex.org/W2797620427"],"related_works":["https://openalex.org/W2576717890","https://openalex.org/W7002757181","https://openalex.org/W2408504390","https://openalex.org/W4393361516","https://openalex.org/W6903186098","https://openalex.org/W3185508530","https://openalex.org/W7097360727","https://openalex.org/W7101241116","https://openalex.org/W6958370951","https://openalex.org/W7095654788"],"abstract_inverted_index":{"Phylogenetic":[0],"trees":[1,224],"are":[2,53,203,208],"graph-like":[3],"structures":[4,252],"whose":[5],"topology":[6],"describes":[7],"the":[8,39,58,78,87,90,93,100,115,153,163,187,237],"inferred":[9],"pattern":[10,59],"of":[11,16,26,34,44,60,66,80,102,146,155,159,186,190,201,223,232,234,263,265],"relationships":[12,61],"among":[13,47,62],"a":[14,63,103,156,184,216,247],"set":[15,43],"biological":[17],"entities,":[18],"such":[19,121],"as":[20,136,183],"species":[21],"or":[22,42],"DNA":[23],"sequences.":[24],"Inference":[25],"these":[27,266],"phylogenies":[28],"typically":[29],"involves":[30],"evaluating":[31],"large":[32,64,81,147],"numbers":[33],"possible":[35],"solutions":[36,132],"and":[37,140,180,225,236,253],"choosing":[38],"optimal":[40],"topology,":[41,198],"topologies,":[45],"from":[46],"all":[48],"evaluated":[49],"solutions.":[50],"Such":[51],"analyses":[52],"computationally":[54],"intensive,":[55],"especially":[56],"when":[57],"number":[65],"entities":[67],"is":[68,84,150,173],"being":[69],"sought.":[70],"This":[71],"thesis":[72,243],"introduces":[73],"two":[74],"novel":[75,157,217],"algorithms":[76,110,129],"for":[77,166,256],"inference":[79,149],"trees;":[82],"one":[83],"applicable":[85],"to":[86,92,169,195],"likelihood":[88],"framework,":[89],"other":[91],"Bayesian":[94],"framework.":[95],"Both":[96],"approaches":[97],"rely":[98],"on":[99,175,210],"notion":[101],"multi-modal":[104],"tree":[105],"\u2018landscape\u2019":[106],"through":[107],"which":[108],"inferential":[109],"traverse.":[111],"Using":[112],"sampling":[113],"techniques,":[114],"landscape":[116],"can":[117,125],"be":[118,126],"perturbed":[119],"sequentially,":[120],"that":[122],"local":[123],"optima":[124],"evaded.":[127],"The":[128,171,242,258],"find":[130],"good":[131],"in":[133,152,230,268],"reasonable":[134],"time,":[135],"demonstrated":[137],"using":[138,215],"real":[139],"simulated":[141],"data":[142,235,251],"sets.":[143],"An":[144],"example":[145],"phylogeny":[148,161,172],"presented":[151,219],"form":[154],"estimate":[158,165],"Primate":[160,191],"\u2013":[162],"largest":[164],"this":[167,196],"Order":[168],"date.":[170],"based":[174,209],"previously":[176],"published":[177],"smaller":[178],"phylogenies,":[179],"hence":[181],"serves":[182],"summary":[185],"present":[188],"state":[189],"phylogeny.":[192],"In":[193],"addition":[194],"\u2018supertree\u2019s\u2019":[197],"composite":[199],"estimates":[200,207],"divergence":[202],"provided":[204],"also.":[205],"These":[206],"multiple,":[211],"clock-like":[212],"genes":[213],"combined":[214],"approach":[218],"here.":[220],"Handling":[221],"sets":[222],"sequences":[226],"poses":[227],"practical":[228],"problems":[229],"terms":[231],"conversion":[233],"interoperation":[238],"between":[239],"computer":[240],"programs.":[241],"therefore":[244],"concludes":[245],"with":[246],"chapter":[248],"discussing":[249],"suitable":[250],"programming":[254,272],"patterns":[255],"phylogenetics.":[257],"appendix":[259],"discusses":[260],"an":[261,269],"implementation":[262],"some":[264],"concepts":[267],"object-oriented":[270],"application":[271],"interface.":[273]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-11-08T12:12:28.789561","created_date":"2016-06-24T00:00:00"}