{"id":"https://openalex.org/W1969636905","doi":"https://doi.org/10.1109/fpl.2014.6927430","title":"An FPGA hardware acceleration of the indirect calculation of tree lengths method for phylogenetic tree reconstruction","display_name":"An FPGA hardware acceleration of the indirect calculation of tree lengths method for phylogenetic tree reconstruction","publication_year":2014,"publication_date":"2014-09-01","ids":{"openalex":"https://openalex.org/W1969636905","doi":"https://doi.org/10.1109/fpl.2014.6927430","mag":"1969636905"},"language":"en","primary_location":{"id":"doi:10.1109/fpl.2014.6927430","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpl.2014.6927430","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 24th International Conference on Field Programmable Logic and Applications (FPL)","raw_type":"proceedings-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/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":["Systems and Information Engineering, University of Tsukuba, Tsukuba, JAPAN","Systems and Information Engineering, University of Tsukuba, 1-1-1 Ten-ou-dai 305-8573 JAPAN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Systems and Information Engineering, University of Tsukuba, Tsukuba, JAPAN","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"Systems and Information Engineering, University of Tsukuba, 1-1-1 Ten-ou-dai 305-8573 JAPAN","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":["Systems and Information Engineering, University of Tsukuba, Tsukuba, JAPAN","Systems and Information Engineering, University of Tsukuba, 1-1-1 Ten-ou-dai 305-8573 JAPAN"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Systems and Information Engineering, University of Tsukuba, Tsukuba, JAPAN","institution_ids":["https://openalex.org/I146399215"]},{"raw_affiliation_string":"Systems and Information Engineering, University of Tsukuba, 1-1-1 Ten-ou-dai 305-8573 JAPAN","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":0.4269,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.62442954,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"99","issue":null,"first_page":"1","last_page":"4"},"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/T10434","display_name":"Chromosomal and Genetic Variations","score":0.9922999739646912,"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"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9884999990463257,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/acceleration","display_name":"Acceleration","score":0.7826772332191467},{"id":"https://openalex.org/keywords/field-programmable-gate-array","display_name":"Field-programmable gate array","score":0.717168390750885},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.6816145777702332},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6696488261222839},{"id":"https://openalex.org/keywords/pipeline","display_name":"Pipeline (software)","score":0.6477629542350769},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.590155839920044},{"id":"https://openalex.org/keywords/hardware-acceleration","display_name":"Hardware acceleration","score":0.5509308576583862},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.5390201807022095},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.46614566445350647},{"id":"https://openalex.org/keywords/base","display_name":"Base (topology)","score":0.41125333309173584},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.34467950463294983},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3297584056854248},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.28679054975509644},{"id":"https://openalex.org/keywords/computer-hardware","display_name":"Computer hardware","score":0.19816994667053223},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.1472100019454956},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.11323526501655579},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07003283500671387},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.06642943620681763}],"concepts":[{"id":"https://openalex.org/C117896860","wikidata":"https://www.wikidata.org/wiki/Q11376","display_name":"Acceleration","level":2,"score":0.7826772332191467},{"id":"https://openalex.org/C42935608","wikidata":"https://www.wikidata.org/wiki/Q190411","display_name":"Field-programmable gate array","level":2,"score":0.717168390750885},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.6816145777702332},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6696488261222839},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.6477629542350769},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.590155839920044},{"id":"https://openalex.org/C13164978","wikidata":"https://www.wikidata.org/wiki/Q600158","display_name":"Hardware acceleration","level":3,"score":0.5509308576583862},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.5390201807022095},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.46614566445350647},{"id":"https://openalex.org/C42058472","wikidata":"https://www.wikidata.org/wiki/Q810214","display_name":"Base (topology)","level":2,"score":0.41125333309173584},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.34467950463294983},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3297584056854248},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.28679054975509644},{"id":"https://openalex.org/C9390403","wikidata":"https://www.wikidata.org/wiki/Q3966","display_name":"Computer hardware","level":1,"score":0.19816994667053223},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.1472100019454956},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.11323526501655579},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07003283500671387},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.06642943620681763},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","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/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/fpl.2014.6927430","is_oa":false,"landing_page_url":"https://doi.org/10.1109/fpl.2014.6927430","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2014 24th International Conference on Field Programmable Logic and Applications (FPL)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1972390207","https://openalex.org/W2030517987","https://openalex.org/W2079091049","https://openalex.org/W2083213362","https://openalex.org/W2099748572","https://openalex.org/W2121633297","https://openalex.org/W2151692850","https://openalex.org/W2167934704","https://openalex.org/W2169616042","https://openalex.org/W2316705841","https://openalex.org/W4205208900","https://openalex.org/W4205819726","https://openalex.org/W4206702770","https://openalex.org/W4230350175","https://openalex.org/W4231060015","https://openalex.org/W4254717640","https://openalex.org/W6674970839"],"related_works":["https://openalex.org/W2160069347","https://openalex.org/W2361394567","https://openalex.org/W4363649491","https://openalex.org/W1517776641","https://openalex.org/W2057084000","https://openalex.org/W2600063918","https://openalex.org/W2359405402","https://openalex.org/W2025227071","https://openalex.org/W1995457609","https://openalex.org/W4293225502"],"abstract_inverted_index":{"In":[0,42],"this":[1],"work,":[2],"we":[3,45],"present":[4],"an":[5],"FPGA":[6],"hardware":[7,74],"implementation":[8],"for":[9,62,95,117,133],"a":[10,23,47],"phylogenetic":[11],"tree":[12,48],"reconstruction":[13],"with":[14],"maximum":[15],"parsimony":[16,81],"algorithm.":[17],"We":[18,59,67,125],"base":[19],"our":[20,43,72,102],"approach":[21],"on":[22],"particular":[24],"stochastic":[25],"local":[26],"search":[27,53],"algorithm":[28],"that":[29,127],"uses":[30],"the":[31,39,52,78,96,118],"Indirect":[32],"Calculation":[33],"of":[34],"Tree":[35],"Lengths":[36],"method":[37],"and":[38,50,56,76,91,113],"Progressive":[40],"Neighborhood.":[41],"implementation,":[44],"define":[46],"structure,":[49],"accelerate":[51],"by":[54],"parallel":[55],"pipeline":[57],"processing.":[58],"show":[60],"results":[61],"six":[63],"real-world":[64],"biological":[65],"datasets.":[66,136],"compare":[68],"execution":[69],"times":[70],"against":[71,101,123],"previous":[73,103],"approach,":[75],"TNT,":[77],"fastest":[79],"available":[80],"program.":[82],"Acceleration":[83,105],"rates":[84,106,130],"between":[85,107],"34":[86],"to":[87,93,109,115],"45":[88],"per":[89,111],"rearrangement,":[90,112],"2":[92,108],"6,":[94],"whole":[97,119],"search,":[98,120],"are":[99,121],"obtained":[100,122],"approach.":[104],"4":[110],"18":[114],"112,":[116],"TNT.":[124],"estimate":[126],"these":[128],"acceleration":[129],"could":[131],"increase":[132],"even":[134],"larger":[135]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}