{"id":"https://openalex.org/W2011600747","doi":"https://doi.org/10.1145/2460216.2460226","title":"High performance phylogenetic analysis on CUDA-compatible GPUs","display_name":"High performance phylogenetic analysis on CUDA-compatible GPUs","publication_year":2012,"publication_date":"2012-03-25","ids":{"openalex":"https://openalex.org/W2011600747","doi":"https://doi.org/10.1145/2460216.2460226","mag":"2011600747"},"language":"en","primary_location":{"id":"doi:10.1145/2460216.2460226","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2460216.2460226","pdf_url":null,"source":{"id":"https://openalex.org/S4210193905","display_name":"ACM SIGARCH Computer Architecture News","issn_l":"0163-5964","issn":["0163-5964","1943-5851"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320740","host_organization_name":"ACM SIGARCH","host_organization_lineage":["https://openalex.org/P4310320740"],"host_organization_lineage_names":["ACM SIGARCH"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM SIGARCH Computer Architecture News","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"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/A5101935082","display_name":"Cheng Ling","orcid":"https://orcid.org/0000-0003-3827-849X"},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Cheng Ling","raw_affiliation_strings":["The University of Edinburgh","the University of Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Edinburgh","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"the University of Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104706884","display_name":"Khaled Benkrid","orcid":null},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Khaled Benkrid","raw_affiliation_strings":["The University of Edinburgh","the University of Edinburgh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The University of Edinburgh","institution_ids":["https://openalex.org/I98677209"]},{"raw_affiliation_string":"the University of Edinburgh","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108833859","display_name":"Tsuyoshi Hamada","orcid":null},"institutions":[{"id":"https://openalex.org/I43777268","display_name":"Nagasaki University","ror":"https://ror.org/058h74p94","country_code":"JP","type":"education","lineage":["https://openalex.org/I43777268"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tsuyoshi Hamada","raw_affiliation_strings":["Nagasaki University","#N##TAB##TAB##TAB##TAB# Nagasaki University#N##TAB##TAB##TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nagasaki University","institution_ids":["https://openalex.org/I43777268"]},{"raw_affiliation_string":"#N##TAB##TAB##TAB##TAB# Nagasaki University#N##TAB##TAB##TAB#","institution_ids":["https://openalex.org/I43777268"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.07546087,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"40","issue":"5","first_page":"52","last_page":"57"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9997000098228455,"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":0.9997000098228455,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9894999861717224,"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/T14049","display_name":"Plant and Fungal Species Descriptions","score":0.9606999754905701,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.7351218461990356},{"id":"https://openalex.org/keywords/cuda","display_name":"CUDA","score":0.7277993559837341},{"id":"https://openalex.org/keywords/xeon","display_name":"Xeon","score":0.7257199883460999},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6809879541397095},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.6584550142288208},{"id":"https://openalex.org/keywords/markov-chain-monte-carlo","display_name":"Markov chain Monte Carlo","score":0.5800997614860535},{"id":"https://openalex.org/keywords/xeon-phi","display_name":"Xeon Phi","score":0.5115628838539124},{"id":"https://openalex.org/keywords/speedup","display_name":"Speedup","score":0.48444226384162903},{"id":"https://openalex.org/keywords/general-purpose-computing-on-graphics-processing-units","display_name":"General-purpose computing on graphics processing units","score":0.4518342912197113},{"id":"https://openalex.org/keywords/markov-chain","display_name":"Markov chain","score":0.41918259859085083},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.41486573219299316},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3957449793815613},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3853563666343689},{"id":"https://openalex.org/keywords/graphics","display_name":"Graphics","score":0.1823500096797943},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16935691237449646},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.15697386860847473},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.12227863073348999},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.1036214828491211},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.10199770331382751}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.7351218461990356},{"id":"https://openalex.org/C2778119891","wikidata":"https://www.wikidata.org/wiki/Q477690","display_name":"CUDA","level":2,"score":0.7277993559837341},{"id":"https://openalex.org/C145108525","wikidata":"https://www.wikidata.org/wiki/Q656154","display_name":"Xeon","level":2,"score":0.7257199883460999},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6809879541397095},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.6584550142288208},{"id":"https://openalex.org/C111350023","wikidata":"https://www.wikidata.org/wiki/Q1191869","display_name":"Markov chain Monte Carlo","level":3,"score":0.5800997614860535},{"id":"https://openalex.org/C96972482","wikidata":"https://www.wikidata.org/wiki/Q1049168","display_name":"Xeon Phi","level":2,"score":0.5115628838539124},{"id":"https://openalex.org/C68339613","wikidata":"https://www.wikidata.org/wiki/Q1549489","display_name":"Speedup","level":2,"score":0.48444226384162903},{"id":"https://openalex.org/C50630238","wikidata":"https://www.wikidata.org/wiki/Q971505","display_name":"General-purpose computing on graphics processing units","level":3,"score":0.4518342912197113},{"id":"https://openalex.org/C98763669","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov chain","level":2,"score":0.41918259859085083},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.41486573219299316},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3957449793815613},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3853563666343689},{"id":"https://openalex.org/C21442007","wikidata":"https://www.wikidata.org/wiki/Q1027879","display_name":"Graphics","level":2,"score":0.1823500096797943},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16935691237449646},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.15697386860847473},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.12227863073348999},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.1036214828491211},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.10199770331382751},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/2460216.2460226","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2460216.2460226","pdf_url":null,"source":{"id":"https://openalex.org/S4210193905","display_name":"ACM SIGARCH Computer Architecture News","issn_l":"0163-5964","issn":["0163-5964","1943-5851"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320740","host_organization_name":"ACM SIGARCH","host_organization_lineage":["https://openalex.org/P4310320740"],"host_organization_lineage_names":["ACM SIGARCH"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM SIGARCH Computer Architecture News","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W2088481129","https://openalex.org/W2097706568","https://openalex.org/W2102424972","https://openalex.org/W2106882534","https://openalex.org/W2117443107","https://openalex.org/W2124686949","https://openalex.org/W2136485386","https://openalex.org/W2138309709","https://openalex.org/W2156521045","https://openalex.org/W4254717640","https://openalex.org/W4300476846"],"related_works":["https://openalex.org/W2623711278","https://openalex.org/W2695396743","https://openalex.org/W2166164399","https://openalex.org/W2037963718","https://openalex.org/W2256606255","https://openalex.org/W3142517318","https://openalex.org/W1445273741","https://openalex.org/W3007055187","https://openalex.org/W2205865923","https://openalex.org/W2086841337"],"abstract_inverted_index":{"The":[0,105,122],"operation":[1,35],"of":[2,21,39,50,59,85,101,112],"phylogenetic":[3,28,71,96,117],"analysis":[4,29,97,118],"aims":[5],"to":[6,55,137],"investigate":[7],"the":[8,19,37,48,56,62,65,78,110,113],"evolution":[9],"and":[10,24,83,156],"relationships":[11],"among":[12],"species.":[13],"It":[14],"is":[15,30,107],"widely":[16,115],"used":[17,116],"in":[18,43,61,126],"fields":[20],"system":[22],"biology":[23],"comparative":[25],"genomics.":[26],"However,":[27],"also":[31],"a":[32,44,86,99,145,149],"computationally":[33],"intensive":[34],"as":[36],"number":[38,49,58],"tree":[40],"topology":[41],"grows":[42],"factorial":[45],"way":[46],"with":[47,148],"species":[51,60],"involved.":[52],"Therefore,":[53],"due":[54],"large":[57],"real":[63],"world,":[64],"computational":[66],"burden":[67],"has":[68],"largely":[69],"thwarted":[70],"reconstruction.":[72],"In":[73],"this":[74],"paper,":[75],"we":[76],"describe":[77],"detailed":[79],"GPU-based":[80],"multi-threaded":[81],"design":[82],"implementation":[84,106,142],"Markov":[87],"Chain":[88],"Monte":[89],"Carlo":[90],"(MCMC)":[91],"maximum":[92],"likelihood":[93],"algorithm":[94],"for":[95],"on":[98,109,129,144],"set":[100],"aligned":[102],"nucleotide":[103],"sequences.":[104],"based":[108],"framework":[111],"most":[114],"tool,":[119],"namely":[120],"MrBayes.":[121],"proposed":[123],"approach":[124],"resulted":[125],"6x-8x":[127],"speed-up":[128],"an":[130,138],"NVidia":[131],"Geforce":[132],"460":[133],"GTX":[134],"GPU":[135],"compared":[136],"optimized":[139],"GPP-based":[140],"software":[141],"running":[143],"desktop":[146],"computer":[147],"single":[150],"Intel":[151],"Xeon":[152],"2.53":[153],"GHz":[154],"CPU":[155],"6.0":[157],"GB":[158],"RAM.":[159]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}