{"id":"https://openalex.org/W2463238764","doi":"https://doi.org/10.1177/1094342016652461","title":"MrBayes sMC<sup>3</sup>","display_name":"MrBayes sMC<sup>3</sup>","publication_year":2016,"publication_date":"2016-06-30","ids":{"openalex":"https://openalex.org/W2463238764","doi":"https://doi.org/10.1177/1094342016652461","mag":"2463238764"},"language":"en","primary_location":{"id":"doi:10.1177/1094342016652461","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342016652461","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","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/A5008373958","display_name":"L\u00eddia Kuan","orcid":null},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":true,"raw_author_name":"L\u00eddia Kuan","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078717814","display_name":"Frederico Pratas","orcid":null},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Frederico Pratas","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5077537777","display_name":"Leonel Sousa","orcid":"https://orcid.org/0000-0002-8066-221X"},"institutions":[{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]},{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Leonel Sousa","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5075054918","display_name":"Pedro Tom\u00e1s","orcid":"https://orcid.org/0000-0001-8083-4432"},"institutions":[{"id":"https://openalex.org/I121345201","display_name":"Instituto de Engenharia de Sistemas e Computadores Investiga\u00e7\u00e3o e Desenvolvimento","ror":"https://ror.org/04mqy3p58","country_code":"PT","type":"nonprofit","lineage":["https://openalex.org/I121345201","https://openalex.org/I4210125590"]},{"id":"https://openalex.org/I141596103","display_name":"University of Lisbon","ror":"https://ror.org/01c27hj86","country_code":"PT","type":"education","lineage":["https://openalex.org/I141596103"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Pedro Tom\u00e1s","raw_affiliation_strings":["INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal"],"affiliations":[{"raw_affiliation_string":"INESC-ID, Instituto Superior T\u00e9cnico, Universidade de Lisboa, Portugal","institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5008373958"],"corresponding_institution_ids":["https://openalex.org/I121345201","https://openalex.org/I141596103"],"apc_list":null,"apc_paid":null,"fwci":0.5002,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.70355103,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"32","issue":"2","first_page":"246","last_page":"265"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9918000102043152,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9754999876022339,"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/computer-science","display_name":"Computer science","score":0.577569842338562},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5681256651878357},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5552800297737122},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.4397445321083069},{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.43669477105140686},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24305418133735657}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.577569842338562},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5681256651878357},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5552800297737122},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.4397445321083069},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.43669477105140686},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24305418133735657},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1177/1094342016652461","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342016652461","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W192467300","https://openalex.org/W1853545769","https://openalex.org/W1965942711","https://openalex.org/W1984296775","https://openalex.org/W2006593001","https://openalex.org/W2033052394","https://openalex.org/W2036748090","https://openalex.org/W2058389929","https://openalex.org/W2063099138","https://openalex.org/W2083005303","https://openalex.org/W2094710165","https://openalex.org/W2102424972","https://openalex.org/W2119632499","https://openalex.org/W2124686949","https://openalex.org/W2124790653","https://openalex.org/W2125359798","https://openalex.org/W2138309709","https://openalex.org/W2148698435","https://openalex.org/W2151142801","https://openalex.org/W2154865023","https://openalex.org/W2158847865","https://openalex.org/W2161444534","https://openalex.org/W2165140440","https://openalex.org/W2168696662","https://openalex.org/W2169943826","https://openalex.org/W2169981472","https://openalex.org/W2255933462","https://openalex.org/W3199943451"],"related_works":["https://openalex.org/W1604898313","https://openalex.org/W2034393996","https://openalex.org/W2164287667","https://openalex.org/W4233815414","https://openalex.org/W2140418760","https://openalex.org/W2581223690","https://openalex.org/W2372170743","https://openalex.org/W4250047567","https://openalex.org/W1580730938","https://openalex.org/W2624440775"],"abstract_inverted_index":{"MrBayes":[0,31,62,67,84,148],"is":[1,32,163],"a":[2,21,35,43,157],"popular":[3],"software":[4],"package":[5],"for":[6,20,121],"Bayesian":[7],"phylogenetic":[8],"inference,":[9],"which":[10,71],"uses":[11],"an":[12,17,78,122],"iterative":[13],"approach":[14],"to":[15,127,135],"derive":[16],"evolutionary":[18],"tree":[19],"collection":[22],"of":[23,38,42,45,77,118,125,147,153],"species":[24],"whose":[25],"DNA":[26],"sequences":[27],"are":[28,49,54],"known.":[29],"Computationally,":[30],"characterized":[33],"by":[34,142],"large":[36],"number":[37],"iterations,":[39],"each":[40],"composed":[41],"set":[44,117],"tasks":[46],"that":[47,108,152],"isolated":[48],"not":[50],"very":[51],"time-consuming,":[52],"but":[53],"globally":[55],"computationally":[56],"demanding.":[57],"To":[58],"accelerate":[59],"the":[60,74,95,109,115,130,138,144,154],"latest":[61],"3.2,":[63],"this":[64],"paper":[65],"presents":[66],"sMC":[68,85,149],"3":[69,86,150],",":[70],"relies":[72],"on":[73],"computational":[75],"power":[76],"heterogeneous":[79],"CPU+GPU":[80],"platform.":[81],"For":[82],"this,":[83],"exploits":[87],"both":[88],"task":[89],"and":[90,101,133],"data-level":[91],"parallelism":[92],"while":[93],"minimizing":[94],"overheads":[96],"associated":[97],"with":[98,114,151],"kernel":[99],"launches":[100],"CPU-GPU":[102],"data":[103],"transfers.":[104],"Experimental":[105],"results":[106],"indicate":[107],"proposed":[110,116],"parallel":[111],"approach,":[112],"together":[113],"optimizations,":[119],"allow":[120],"application":[123],"acceleration":[124],"up":[126,134],"10\u00d7":[128],"regarding":[129,137],"original":[131],"MrBayes,":[132],"3\u00d7":[136],"Beagle":[139],"Library.":[140],"Furthermore,":[141],"analyzing":[143],"convergence":[145],"rate":[146],"state-of-the-art":[155],"approaches,":[156],"significant":[158],"reduction":[159],"in":[160],"execution":[161],"time":[162],"observed.":[164]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2017,"cited_by_count":3}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
