{"id":"https://openalex.org/W2583713474","doi":"https://doi.org/10.1587/transinf.2015edp7433","title":"FPGA Hardware Acceleration of a Phylogenetic Tree Reconstruction with Maximum Parsimony Algorithm","display_name":"FPGA Hardware Acceleration of a Phylogenetic Tree Reconstruction with Maximum Parsimony Algorithm","publication_year":2017,"publication_date":"2017-01-01","ids":{"openalex":"https://openalex.org/W2583713474","doi":"https://doi.org/10.1587/transinf.2015edp7433","mag":"2583713474"},"language":"en","primary_location":{"id":"doi:10.1587/transinf.2015edp7433","is_oa":true,"landing_page_url":"https://doi.org/10.1587/transinf.2015edp7433","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E100.D/2/E100.D_2015EDP7433/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://www.jstage.jst.go.jp/article/transinf/E100.D/2/E100.D_2015EDP7433/_pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5053673142","display_name":"Henry Block","orcid":null},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Henry BLOCK","raw_affiliation_strings":["Faculty of Engineering, Information and Systems, University of Tsukuba"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Engineering, Information and Systems, University of Tsukuba","institution_ids":["https://openalex.org/I146399215"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102968876","display_name":"Tsutomu Maruyama","orcid":"https://orcid.org/0000-0003-3857-2357"},"institutions":[{"id":"https://openalex.org/I146399215","display_name":"University of Tsukuba","ror":"https://ror.org/02956yf07","country_code":"JP","type":"education","lineage":["https://openalex.org/I146399215"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tsutomu MARUYAMA","raw_affiliation_strings":["Faculty of Engineering, Information and Systems, University of Tsukuba"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Engineering, Information and Systems, University of Tsukuba","institution_ids":["https://openalex.org/I146399215"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I146399215"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.00911887,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"E100.D","issue":"2","first_page":"256","last_page":"264"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998000264167786,"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":0.9998000264167786,"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/T11269","display_name":"Algorithms and Data Compression","score":0.9905999898910522,"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.984000027179718,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7447076439857483},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6723413467407227},{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.6650688052177429},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6170856952667236},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.6137044429779053},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5579248070716858},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5566886067390442},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.530704915523529},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.5257773399353027},{"id":"https://openalex.org/keywords/maximum-parsimony","display_name":"Maximum parsimony","score":0.5158776044845581},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3237028121948242},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.24627196788787842},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.16419804096221924},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.12936845421791077},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.07349878549575806}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7447076439857483},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6723413467407227},{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.6650688052177429},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6170856952667236},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.6137044429779053},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5579248070716858},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5566886067390442},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.530704915523529},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.5257773399353027},{"id":"https://openalex.org/C22799545","wikidata":"https://www.wikidata.org/wiki/Q1805805","display_name":"Maximum parsimony","level":5,"score":0.5158776044845581},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3237028121948242},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.24627196788787842},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.16419804096221924},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.12936845421791077},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.07349878549575806},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C74650414","wikidata":"https://www.wikidata.org/wiki/Q11397","display_name":"Classical mechanics","level":1,"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/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C44465124","wikidata":"https://www.wikidata.org/wiki/Q713623","display_name":"Clade","level":4,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1587/transinf.2015edp7433","is_oa":true,"landing_page_url":"https://doi.org/10.1587/transinf.2015edp7433","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E100.D/2/E100.D_2015EDP7433/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1587/transinf.2015edp7433","is_oa":true,"landing_page_url":"https://doi.org/10.1587/transinf.2015edp7433","pdf_url":"https://www.jstage.jst.go.jp/article/transinf/E100.D/2/E100.D_2015EDP7433/_pdf","source":{"id":"https://openalex.org/S2486202937","display_name":"IEICE Transactions on Information and Systems","issn_l":"0916-8532","issn":["0916-8532","1745-1361"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4320800604","host_organization_name":"Institute of Electronics, Information and Communication Engineers","host_organization_lineage":["https://openalex.org/P4320800604"],"host_organization_lineage_names":["Institute of Electronics, Information and Communication Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEICE Transactions on Information and Systems","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Sustainable cities and communities","id":"https://metadata.un.org/sdg/11","score":0.4000000059604645}],"awards":[],"funders":[{"id":"https://openalex.org/F4320312652","display_name":"Willi Hennig Society","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2583713474.pdf","grobid_xml":"https://content.openalex.org/works/W2583713474.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1969636905","https://openalex.org/W1972390207","https://openalex.org/W2025227071","https://openalex.org/W2030517987","https://openalex.org/W2079091049","https://openalex.org/W2083213362","https://openalex.org/W2099748572","https://openalex.org/W2113755305","https://openalex.org/W2121633297","https://openalex.org/W2151692850","https://openalex.org/W2167934704","https://openalex.org/W2169616042","https://openalex.org/W4205208900","https://openalex.org/W4205819726","https://openalex.org/W4206702770","https://openalex.org/W4230350175","https://openalex.org/W4254717640"],"related_works":["https://openalex.org/W2111241003","https://openalex.org/W4200391368","https://openalex.org/W2210979487","https://openalex.org/W2074043759","https://openalex.org/W3042736233","https://openalex.org/W2082487009","https://openalex.org/W2373535795","https://openalex.org/W2146872326","https://openalex.org/W2518118925","https://openalex.org/W3159273459"],"abstract_inverted_index":{"In":[0,59],"this":[1],"paper,":[2],"we":[3,62],"present":[4],"an":[5],"FPGA":[6],"hardware":[7,91,133],"implementation":[8],"for":[9,48,79,124,147],"a":[10,15,24,64],"phylogenetic":[11,53],"tree":[12,54,65],"reconstruction":[13,55],"with":[14],"maximum":[16],"parsimony":[17,98],"algorithm.":[18],"We":[19,76,84],"base":[20],"our":[21,60,89,131],"approach":[22],"on":[23],"particular":[25],"stochastic":[26],"local":[27],"search":[28,70],"algorithm":[29,56],"that":[30],"uses":[31],"the":[32,36,49,52,69,95,105,125,148],"Progressive":[33],"Neighborhood":[34],"and":[35,67,73,93,120,143],"Indirect":[37,106],"Calculation":[38,107],"of":[39,51,108],"Tree":[40,109],"Lengths":[41,110],"method.":[42,111],"This":[43],"method":[44],"is":[45,101],"widely":[46],"used":[47],"acceleration":[50],"in":[57],"software.":[58],"implementation,":[61],"define":[63],"structure":[66],"accelerate":[68],"by":[71,104],"parallel":[72],"pipeline":[74],"processing.":[75],"show":[77],"results":[78],"eight":[80],"real-world":[81],"biological":[82],"datasets.":[83],"compare":[85],"execution":[86],"times":[87],"against":[88,130,153],"previous":[90,132],"approach,":[92],"TNT,":[94],"fastest":[96],"available":[97],"program,":[99],"which":[100],"also":[102],"accelerated":[103],"Acceleration":[112,135],"rates":[113,136],"between":[114,137],"34":[115],"to":[116,122,139,145],"45":[117],"per":[118,141],"rearrangement,":[119,142],"2":[121,138],"6":[123],"whole":[126,149],"search,":[127,150],"are":[128,151],"obtained":[129,152],"approach.":[134],"36":[140],"18":[144],"112":[146],"TNT.":[154]},"counts_by_year":[{"year":2023,"cited_by_count":2}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}