{"id":"https://openalex.org/W3092040572","doi":"https://doi.org/10.1109/tcyb.2020.3020308","title":"Multiobjective Formulation of Multiple Sequence Alignment for Phylogeny Inference","display_name":"Multiobjective Formulation of Multiple Sequence Alignment for Phylogeny Inference","publication_year":2020,"publication_date":"2020-10-12","ids":{"openalex":"https://openalex.org/W3092040572","doi":"https://doi.org/10.1109/tcyb.2020.3020308","mag":"3092040572","pmid":"https://pubmed.ncbi.nlm.nih.gov/33044939"},"language":"en","primary_location":{"id":"doi:10.1109/tcyb.2020.3020308","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcyb.2020.3020308","pdf_url":null,"source":{"id":"https://openalex.org/S4210191041","display_name":"IEEE Transactions on Cybernetics","issn_l":"2168-2267","issn":["2168-2267","2168-2275"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Cybernetics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"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/A5011223872","display_name":"Muhammad Ali Nayeem","orcid":"https://orcid.org/0000-0003-4164-6492"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Muhammad Ali Nayeem","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0003-4164-6492","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063693993","display_name":"Md. Shamsuzzoha Bayzid","orcid":"https://orcid.org/0000-0002-5640-0615"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Md. Shamsuzzoha Bayzid","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080064706","display_name":"Atif Rahman","orcid":"https://orcid.org/0000-0003-1805-3971"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Atif Hasan Rahman","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090604535","display_name":"Rifat Shahriyar","orcid":"https://orcid.org/0000-0001-9540-315X"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"Rifat Shahriyar","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh"],"raw_orcid":"https://orcid.org/0000-0001-9540-315X","affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029174615","display_name":"M. Sohel Rahman","orcid":"https://orcid.org/0000-0001-9419-6478"},"institutions":[{"id":"https://openalex.org/I183697816","display_name":"Bangladesh University of Engineering and Technology","ror":"https://ror.org/05a1qpv97","country_code":"BD","type":"education","lineage":["https://openalex.org/I183697816"]}],"countries":["BD"],"is_corresponding":false,"raw_author_name":"M. Sohel Rahman","raw_affiliation_strings":["Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh","institution_ids":["https://openalex.org/I183697816"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I183697816"],"apc_list":null,"apc_paid":null,"fwci":0.4068,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.59807528,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"52","issue":"5","first_page":"2775","last_page":"2786"},"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":0.9789000153541565,"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/T11764","display_name":"Evolution and Genetic Dynamics","score":0.9732000231742859,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6703621745109558},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.6161144375801086},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6019731760025024},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5807331204414368},{"id":"https://openalex.org/keywords/metric","display_name":"Metric (unit)","score":0.5589954853057861},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.48871803283691406},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48658668994903564},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.477300763130188},{"id":"https://openalex.org/keywords/evolutionary-algorithm","display_name":"Evolutionary algorithm","score":0.4240185618400574},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4237120747566223},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.3433634638786316},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3324930667877197},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3239020109176636},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3129085898399353},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.0818263590335846}],"concepts":[{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6703621745109558},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6161144375801086},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6019731760025024},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5807331204414368},{"id":"https://openalex.org/C176217482","wikidata":"https://www.wikidata.org/wiki/Q860554","display_name":"Metric (unit)","level":2,"score":0.5589954853057861},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.48871803283691406},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48658668994903564},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.477300763130188},{"id":"https://openalex.org/C159149176","wikidata":"https://www.wikidata.org/wiki/Q14489129","display_name":"Evolutionary algorithm","level":2,"score":0.4240185618400574},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4237120747566223},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.3433634638786316},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3324930667877197},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3239020109176636},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3129085898399353},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0818263590335846},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","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},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcyb.2020.3020308","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcyb.2020.3020308","pdf_url":null,"source":{"id":"https://openalex.org/S4210191041","display_name":"IEEE Transactions on Cybernetics","issn_l":"2168-2267","issn":["2168-2267","2168-2275"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Cybernetics","raw_type":"journal-article"},{"id":"pmid:33044939","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33044939","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on cybernetics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":50,"referenced_works":["https://openalex.org/W99430847","https://openalex.org/W228649082","https://openalex.org/W1518025915","https://openalex.org/W1595498733","https://openalex.org/W1646393397","https://openalex.org/W2007668764","https://openalex.org/W2011289056","https://openalex.org/W2016332126","https://openalex.org/W2018975235","https://openalex.org/W2021379620","https://openalex.org/W2022485595","https://openalex.org/W2031611770","https://openalex.org/W2053238889","https://openalex.org/W2056251063","https://openalex.org/W2071460053","https://openalex.org/W2092672051","https://openalex.org/W2096166399","https://openalex.org/W2106882534","https://openalex.org/W2121691652","https://openalex.org/W2126105956","https://openalex.org/W2127322768","https://openalex.org/W2127774996","https://openalex.org/W2132926880","https://openalex.org/W2136570298","https://openalex.org/W2140872496","https://openalex.org/W2141052558","https://openalex.org/W2143381319","https://openalex.org/W2144362290","https://openalex.org/W2152179349","https://openalex.org/W2157451851","https://openalex.org/W2158862451","https://openalex.org/W2166718648","https://openalex.org/W2170831688","https://openalex.org/W2489219000","https://openalex.org/W2536777678","https://openalex.org/W2546852653","https://openalex.org/W2551043114","https://openalex.org/W2587563010","https://openalex.org/W2616987781","https://openalex.org/W2782577096","https://openalex.org/W2803360717","https://openalex.org/W2956090128","https://openalex.org/W2973557667","https://openalex.org/W2998967790","https://openalex.org/W3004476750","https://openalex.org/W3005131379","https://openalex.org/W3012911890","https://openalex.org/W3026407107","https://openalex.org/W3028517753","https://openalex.org/W4231579661"],"related_works":["https://openalex.org/W2051969447","https://openalex.org/W2111937814","https://openalex.org/W2162923930","https://openalex.org/W1482324242","https://openalex.org/W2133116680","https://openalex.org/W2091678889","https://openalex.org/W2029514038","https://openalex.org/W2149492307","https://openalex.org/W1985408726","https://openalex.org/W2314370104"],"abstract_inverted_index":{"Multiple":[0],"sequence":[1],"alignment":[2],"(MSA)":[3],"is":[4,12,29],"a":[5,21,32,99,111,219,238],"preliminary":[6],"task":[7,28],"for":[8,14,120],"estimating":[9],"phylogenies.":[10],"It":[11],"used":[13,166],"homology":[15],"inference":[16],"among":[17],"the":[18,26,46,64,94,130,136,162,175,180,198,214],"sequences":[19],"of":[20,23,70,101,124,132,138],"set":[22,100],"species.":[24],"Generally,":[25],"MSA":[27,71,164],"handled":[30],"as":[31],"single-objective":[33],"optimization":[34],"process.":[35],"The":[36,66],"alignments":[37,47,159,191],"computed":[38],"under":[39],"one":[40],"criterion":[41],"may":[42,200],"be":[43],"different":[44,59],"from":[45,110],"generated":[48],"by":[49,76,161,183],"other":[50],"criteria,":[51],"inferring":[52],"discordant":[53],"homologies":[54],"and":[55,97,187],"thus":[56],"leading":[57],"to":[58,79,193,202,230],"hypothesized":[60],"evolutionary":[61,148],"histories":[62],"relating":[63],"sequences.":[65],"multiobjective":[67],"(MO)":[68],"formulation":[69,123,134],"has":[72,115],"recently":[73],"been":[74,116],"advocated":[75],"several":[77],"researchers,":[78],"address":[80],"this":[81,247],"issue.":[82],"An":[83],"MO":[84,122,133,149,185,228],"approach":[85],"independently":[86],"optimizes":[87],"multiple":[88],"(often":[89],"conflicting)":[90],"objective":[91],"functions":[92],"at":[93],"same":[95],"time":[96],"outputs":[98],"competitive":[102],"alignments.":[103],"However,":[104],"no":[105],"conceptual":[106],"or":[107],"experimental":[108,242],"rational":[109],"real-world":[112],"application":[113],"perspective":[114],"reported":[117],"so":[118],"far":[119],"any":[121],"MSA.":[125],"This":[126],"article":[127],"work":[128],"investigates":[129],"impact":[131],"in":[135,167,172,197,206,225],"context":[137],"an":[139,184],"important":[140],"scientific":[141],"problem,":[142],"namely,":[143],"phylogeny":[144,233],"estimation.":[145],"Employing":[146],"popular":[147,194],"algorithms,":[150],"we":[151,211,236],"show":[152],"that:":[153],"1)":[154],"trees":[155,176],"inferred":[156,177],"based":[157,178],"on":[158,179],"produced":[160],"existing":[163],"methods":[165],"practice":[168],"are":[169],"substantially":[170],"worse":[171],"quality":[173],"than":[174],"alignment's":[181],"output":[182],"algorithm":[186],"2)":[188],"even":[189],"high-quality":[190],"(according":[192],"measures":[195],"available":[196],"literature)":[199],"fail":[201],"achieve":[203],"acceptable":[204],"accuracy":[205],"generating":[207],"phylogenetic":[208],"trees.":[209],"Thus,":[210],"essentially":[212],"ask":[213],"following":[215],"natural":[216],"question:":[217],"\"can":[218],"phylogeny-aware":[220],"(i.e.,":[221],"application-aware)":[222],"metric":[223],"guide":[224],"selecting":[226],"appropriate":[227],"formulations":[229],"ensure":[231],"better":[232],"estimation?\"":[234],"Here,":[235],"report":[237],"carefully":[239],"designed":[240],"extensive":[241],"study":[243],"that":[244],"positively":[245],"answers":[246],"question.":[248]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
