{"id":"https://openalex.org/W2132121343","doi":"https://doi.org/10.1177/1094342013495095","title":"High-performance computing selection of models of DNA substitution for multicore clusters","display_name":"High-performance computing selection of models of DNA substitution for multicore clusters","publication_year":2013,"publication_date":"2013-07-14","ids":{"openalex":"https://openalex.org/W2132121343","doi":"https://doi.org/10.1177/1094342013495095","mag":"2132121343"},"language":"en","primary_location":{"id":"doi:10.1177/1094342013495095","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342013495095","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":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2183/20978","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5087352477","display_name":"Diego Darriba","orcid":"https://orcid.org/0000-0001-5482-3932"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]},{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Diego Darriba","raw_affiliation_strings":["Bioinformatics and Molecular Evolution Group, University of Vigo, Vigo, Spain","Computer Architecture Group, University of A Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Molecular Evolution Group, University of Vigo, Vigo, Spain","institution_ids":["https://openalex.org/I6289922"]},{"raw_affiliation_string":"Computer Architecture Group, University of A Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049011209","display_name":"Guillermo L. Taboada","orcid":"https://orcid.org/0000-0002-6281-6641"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Guillermo L Taboada","raw_affiliation_strings":["Computer Architecture Group, University of A Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Computer Architecture Group, University of A Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070686724","display_name":"Ram\u00f3n Doallo","orcid":"https://orcid.org/0000-0002-6011-3387"},"institutions":[{"id":"https://openalex.org/I11019714","display_name":"Universidade da Coru\u00f1a","ror":"https://ror.org/01qckj285","country_code":"ES","type":"education","lineage":["https://openalex.org/I11019714"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Ram\u00f3n Doallo","raw_affiliation_strings":["Computer Architecture Group, University of A Coru\u00f1a, A Coru\u00f1a, Spain"],"affiliations":[{"raw_affiliation_string":"Computer Architecture Group, University of A Coru\u00f1a, A Coru\u00f1a, Spain","institution_ids":["https://openalex.org/I11019714"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042649313","display_name":"David Posada","orcid":"https://orcid.org/0000-0003-1407-3406"},"institutions":[{"id":"https://openalex.org/I6289922","display_name":"Universidade de Vigo","ror":"https://ror.org/05rdf8595","country_code":"ES","type":"education","lineage":["https://openalex.org/I6289922"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"David Posada","raw_affiliation_strings":["Bioinformatics and Molecular Evolution Group, University of Vigo, Vigo, Spain"],"affiliations":[{"raw_affiliation_string":"Bioinformatics and Molecular Evolution Group, University of Vigo, Vigo, Spain","institution_ids":["https://openalex.org/I6289922"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5087352477"],"corresponding_institution_ids":["https://openalex.org/I11019714","https://openalex.org/I6289922"],"apc_list":null,"apc_paid":null,"fwci":0.9885,"has_fulltext":false,"cited_by_count":8,"citation_normalized_percentile":{"value":0.83422142,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"28","issue":"1","first_page":"112","last_page":"125"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11321","display_name":"Error Correcting Code Techniques","score":0.9937999844551086,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11181","display_name":"Advanced Data Storage Technologies","score":0.983299970626831,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8697514533996582},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7113093137741089},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.7078375816345215},{"id":"https://openalex.org/keywords/multi-core-processor","display_name":"Multi-core processor","score":0.6540801525115967},{"id":"https://openalex.org/keywords/shared-memory","display_name":"Shared memory","score":0.6156858205795288},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.6108058094978333},{"id":"https://openalex.org/keywords/distributed-memory","display_name":"Distributed memory","score":0.5279741883277893},{"id":"https://openalex.org/keywords/supercomputer","display_name":"Supercomputer","score":0.5054152011871338},{"id":"https://openalex.org/keywords/thread","display_name":"Thread (computing)","score":0.4550238251686096},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.15027743577957153}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8697514533996582},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7113093137741089},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.7078375816345215},{"id":"https://openalex.org/C78766204","wikidata":"https://www.wikidata.org/wiki/Q555032","display_name":"Multi-core processor","level":2,"score":0.6540801525115967},{"id":"https://openalex.org/C133875982","wikidata":"https://www.wikidata.org/wiki/Q764810","display_name":"Shared memory","level":2,"score":0.6156858205795288},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.6108058094978333},{"id":"https://openalex.org/C91481028","wikidata":"https://www.wikidata.org/wiki/Q1054686","display_name":"Distributed memory","level":3,"score":0.5279741883277893},{"id":"https://openalex.org/C83283714","wikidata":"https://www.wikidata.org/wiki/Q121117","display_name":"Supercomputer","level":2,"score":0.5054152011871338},{"id":"https://openalex.org/C138101251","wikidata":"https://www.wikidata.org/wiki/Q213092","display_name":"Thread (computing)","level":2,"score":0.4550238251686096},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.15027743577957153}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/1094342013495095","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342013495095","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"},{"id":"pmh:oai:dnet:ruc_________::070ae8b99132fd0b52b92fcb5ec44d5a","is_oa":true,"landing_page_url":"http://hdl.handle.net/2183/20978","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:dnet:ruc_________::070ae8b99132fd0b52b92fcb5ec44d5a","is_oa":true,"landing_page_url":"http://hdl.handle.net/2183/20978","pdf_url":null,"source":{"id":"https://openalex.org/S4306402641","display_name":"LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Cient\u00edficas)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4383465926","host_organization_name":"LA Referencia","host_organization_lineage":["https://openalex.org/I4383465926"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1988888548","https://openalex.org/W1995093426","https://openalex.org/W1996835973","https://openalex.org/W2046808664","https://openalex.org/W2102424972","https://openalex.org/W2103546861","https://openalex.org/W2120611093","https://openalex.org/W2136627618","https://openalex.org/W2138735798","https://openalex.org/W2139134537","https://openalex.org/W2142635246","https://openalex.org/W2154284350","https://openalex.org/W2155196220","https://openalex.org/W2168175751","https://openalex.org/W2168440447","https://openalex.org/W2172057351","https://openalex.org/W2208566223"],"related_works":["https://openalex.org/W2026512611","https://openalex.org/W1985165680","https://openalex.org/W4245497162","https://openalex.org/W1979099492","https://openalex.org/W2353146130","https://openalex.org/W1990817968","https://openalex.org/W4205439893","https://openalex.org/W2150064838","https://openalex.org/W1933089384","https://openalex.org/W2185094550"],"abstract_inverted_index":{"This":[0,192],"paper":[1,225],"presents":[2],"the":[3,10,16,77,95,101,117,120,124,136,144,175,187,198,215],"high-performance":[4],"computing":[5],"(HPC)":[6],"support":[7],"of":[8,19,21,34,73,94,116,123,143,153,174,178,201,214,220],"jModelTest2,":[9],"most":[11,145],"popular":[12],"bioinformatic":[13],"tool":[14],"for":[15,42,49,57,71,186],"statistical":[17],"selection":[18],"models":[20],"DNA":[22],"substitution.":[23],"As":[24],"this":[25,133,154,224],"can":[26,193],"demand":[27],"vast":[28],"computational":[29,121],"resources,":[30],"especially":[31],"in":[32,119,197,223],"terms":[33],"processing":[35],"power,":[36],"jModelTest2":[37,221],"implements":[38],"three":[39,216],"parallel":[40,217],"algorithms":[41],"model":[43,86,147],"selection:":[44],"(1)":[45],"a":[46,54,66,84,113,140,158,165,195,229],"multithreaded":[47,85,176],"implementation":[48,56,70,213],"shared":[50,96,160],"memory":[51,59,69,130,161,190],"architectures;":[52],"(2)":[53],"message-passing":[55],"distributed":[58,98],"architectures,":[60],"such":[61],"as":[62],"clusters;":[63],"and":[64,97,163,182],"(3)":[65],"hybrid":[67,128,188],"shared/distributed":[68,129,189],"clusters":[72],"multicore":[74],"nodes,":[75],"combining":[76],"workload":[78,102,137],"distribution":[79],"across":[80],"cluster":[81,167],"nodes":[82],"with":[83,172],"optimization":[87,148],"within":[88],"each":[89],"node.":[90],"The":[91,127,150,212],"main":[92],"limitation":[93],"versions":[99],"is":[100],"imbalance":[103,138],"that":[104],"generally":[105],"appears":[106],"when":[107],"using":[108],"more":[109],"than":[110],"32":[111],"cores,":[112],"direct":[114],"consequence":[115],"heterogeneity":[118],"cost":[122],"evaluated":[125],"models.":[126],"version":[131,177],"overcomes":[132],"issue":[134],"reducing":[135],"through":[139],"thread-based":[141],"decomposition":[142],"costly":[146],"tasks.":[149],"performance":[151],"evaluation":[152],"HPC":[155],"application":[156],"on":[157,164],"40-core":[159],"system":[162],"528-core":[166],"has":[168],"shown":[169],"high":[170],"scalability,":[171],"speedups":[173],"up":[179,183],"to":[180,184,208],"32,":[181],"257":[185],"implementation.":[191],"represent":[194],"reduction":[196],"execution":[199,218],"time":[200],"some":[202],"analyses":[203],"from":[204],"4":[205],"days":[206],"down":[207],"barely":[209],"20":[210],"minutes.":[211],"strategies":[219],"presented":[222],"are":[226],"available":[227],"under":[228],"GPL":[230],"license":[231],"at":[232],"http://code.google.com/jmodeltest2.":[233]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
