{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T04:28:51Z","timestamp":1750220931137,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":37,"publisher":"ACM","license":[{"start":{"date-parts":[[2019,7,13]],"date-time":"2019-07-13T00:00:00Z","timestamp":1562976000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"ICT Division, Government of People?s Republic of Bangladesh"}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2019,7,13]]},"DOI":"10.1145\/3321707.3321773","type":"proceedings-article","created":{"date-parts":[[2019,7,3]],"date-time":"2019-07-03T13:48:04Z","timestamp":1562161684000},"page":"577-585","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["A 'phylogeny-aware' multi-objective optimization approach for computing MSA"],"prefix":"10.1145","author":[{"given":"Muhammad Ali","family":"Nayeem","sequence":"first","affiliation":[{"name":"BUET, Dhaka, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Md. Shamsuzzoha","family":"Bayzid","sequence":"additional","affiliation":[{"name":"BUET, Dhaka, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Atif Hasan","family":"Rahman","sequence":"additional","affiliation":[{"name":"BUET, Dhaka, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rifat","family":"Shahriyar","sequence":"additional","affiliation":[{"name":"BUET, Dhaka, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M. Sohel","family":"Rahman","sequence":"additional","affiliation":[{"name":"BUET, Dhaka, Bangladesh"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"320","published-online":{"date-parts":[[2019,7,13]]},"reference":[{"key":"e_1_3_2_2_1_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt098"},{"key":"e_1_3_2_2_2_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-16480-9_18"},{"key":"e_1_3_2_2_3_1","volume-title":"Fast statistical alignment. PLoS computational biology 5, 5","author":"Bradley Robert K","year":"2009","unstructured":"Robert K Bradley , Adam Roberts , Michael Smoot , Sudeep Juvekar , Jaeyoung Do , Colin Dewey , Ian Holmes , and Lior Pachter . 2009. Fast statistical alignment. PLoS computational biology 5, 5 ( 2009 ), e1000392. Robert K Bradley, Adam Roberts, Michael Smoot, Sudeep Juvekar, Jaeyoung Do, Colin Dewey, Ian Holmes, and Lior Pachter. 2009. Fast statistical alignment. PLoS computational biology 5, 5 (2009), e1000392."},{"key":"e_1_3_2_2_4_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10489-009-0189-4"},{"key":"e_1_3_2_2_5_1","doi-asserted-by":"publisher","DOI":"10.1109\/TEVC.2013.2281535"},{"key":"e_1_3_2_2_6_1","doi-asserted-by":"publisher","DOI":"10.1109\/4235.996017"},{"key":"e_1_3_2_2_7_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.swevo.2011.02.002"},{"key":"e_1_3_2_2_8_1","volume-title":"Michael Brudno, and Serafim Batzoglou.","author":"Do Chuong B","year":"2005","unstructured":"Chuong B Do , Mahathi SP Mahabhashyam , Michael Brudno, and Serafim Batzoglou. 2005 . ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome research 15, 2 (2005), 330--340. Chuong B Do, Mahathi SP Mahabhashyam, Michael Brudno, and Serafim Batzoglou. 2005. ProbCons: Probabilistic consistency-based multiple sequence alignment. Genome research 15, 2 (2005), 330--340."},{"key":"e_1_3_2_2_9_1","volume-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32, 5","author":"Edgar Robert C","year":"2004","unstructured":"Robert C Edgar . 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32, 5 ( 2004 ), 1792--1797. Robert C Edgar. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids research 32, 5 (2004), 1792--1797."},{"key":"e_1_3_2_2_10_1","doi-asserted-by":"publisher","DOI":"10.1080\/01621459.1937.10503522"},{"key":"e_1_3_2_2_11_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.89.22.10915"},{"key":"e_1_3_2_2_12_1","volume-title":"A simple sequentially rejective multiple test procedure. Scandinavian journal of statistics","author":"Holm Sture","year":"1979","unstructured":"Sture Holm . 1979. A simple sequentially rejective multiple test procedure. Scandinavian journal of statistics ( 1979 ), 65--70. Sture Holm. 1979. A simple sequentially rejective multiple test procedure. Scandinavian journal of statistics (1979), 65--70."},{"volume-title":"Multi objective optimization using evolutionary algorithms","author":"Kalyanmoy Deb","key":"e_1_3_2_2_13_1","unstructured":"Deb Kalyanmoy . 2001. Multi objective optimization using evolutionary algorithms . John Wiley and Sons . Deb Kalyanmoy. 2001. Multi objective optimization using evolutionary algorithms. John Wiley and Sons."},{"key":"e_1_3_2_2_14_1","volume-title":"MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 14","author":"Katoh Kazutaka","year":"2002","unstructured":"Kazutaka Katoh , Kazuharu Misawa , Kei-ichi Kuma, and Takashi Miyata . 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 14 ( 2002 ), 3059--3066. Kazutaka Katoh, Kazuharu Misawa, Kei-ichi Kuma, and Takashi Miyata. 2002. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic acids research 30, 14 (2002), 3059--3066."},{"key":"e_1_3_2_2_15_1","volume-title":"Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic acids research 37, 3","author":"Lassmann Timo","year":"2008","unstructured":"Timo Lassmann , Oliver Frings , and Erik LL Sonnhammer . 2008. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic acids research 37, 3 ( 2008 ), 858--865. Timo Lassmann, Oliver Frings, and Erik LL Sonnhammer. 2008. Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features. Nucleic acids research 37, 3 (2008), 858--865."},{"key":"e_1_3_2_2_16_1","volume-title":"Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324, 5934","author":"Liu Kevin","year":"2009","unstructured":"Kevin Liu , Sindhu Raghavan , Serita Nelesen , C Randal Linder , and Tandy Warnow . 2009. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324, 5934 ( 2009 ), 1561--1564. Kevin Liu, Sindhu Raghavan, Serita Nelesen, C Randal Linder, and Tandy Warnow. 2009. Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324, 5934 (2009), 1561--1564."},{"key":"e_1_3_2_2_17_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq338"},{"key":"e_1_3_2_2_18_1","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0409137102"},{"key":"e_1_3_2_2_19_1","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2014.0156"},{"volume-title":"Introduction to linear regression analysis","author":"Montgomery Douglas C","key":"e_1_3_2_2_20_1","unstructured":"Douglas C Montgomery , Elizabeth A Peck , and G Geoffrey Vining . 2012. Introduction to linear regression analysis . Vol. 821 . John Wiley & Sons . Douglas C Montgomery, Elizabeth A Peck, and G Geoffrey Vining. 2012. Introduction to linear regression analysis. Vol. 821. John Wiley & Sons."},{"key":"e_1_3_2_2_21_1","doi-asserted-by":"publisher","DOI":"10.1006\/jmbi.2000.4042"},{"key":"e_1_3_2_2_22_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btt360"},{"key":"e_1_3_2_2_23_1","volume-title":"MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic acids research 34, 16","author":"Pei Jimin","year":"2006","unstructured":"Jimin Pei and Nick V Grishin . 2006. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic acids research 34, 16 ( 2006 ), 4364--4374. Jimin Pei and Nick V Grishin. 2006. MUMMALS: multiple sequence alignment improved by using hidden Markov models with local structural information. Nucleic acids research 34, 16 (2006), 4364--4374."},{"key":"e_1_3_2_2_24_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btl472"},{"key":"e_1_3_2_2_25_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCYB.2016.2621129"},{"key":"e_1_3_2_2_26_1","doi-asserted-by":"publisher","DOI":"10.1109\/TEVC.2015.2469546"},{"key":"e_1_3_2_2_27_1","doi-asserted-by":"crossref","unstructured":"David J Sheskin. 2003. Handbook of parametric and nonparametric statistical procedures. crc Press.   David J Sheskin. 2003. Handbook of parametric and nonparametric statistical procedures. crc Press.","DOI":"10.1201\/9781420036268"},{"key":"e_1_3_2_2_28_1","doi-asserted-by":"crossref","unstructured":"Fabian Sievers Andreas Wilm David Dineen Toby J Gibson Kevin Karplus Weizhong Li Rodrigo Lopez Hamish McWilliam Michael Remmert Johannes S\u00f6ding etal 2011. Fast scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular systems biology 7 1 (2011) 539.  Fabian Sievers Andreas Wilm David Dineen Toby J Gibson Kevin Karplus Weizhong Li Rodrigo Lopez Hamish McWilliam Michael Remmert Johannes S\u00f6ding et al. 2011. Fast scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Molecular systems biology 7 1 (2011) 539.","DOI":"10.1038\/msb.2011.75"},{"key":"e_1_3_2_2_29_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-12418-6_10"},{"key":"e_1_3_2_2_30_1","volume-title":"Reticular alignment: A progressive corner-cutting method for multiple sequence alignment. BMC bioinformatics 11, 1","author":"Szab\u00f3 Adrienn","year":"2010","unstructured":"Adrienn Szab\u00f3 , \u00c1d\u00e1m Nov\u00e1k , Istv\u00e1n Mikl\u00f3s , and Jotun Hein . 2010. Reticular alignment: A progressive corner-cutting method for multiple sequence alignment. BMC bioinformatics 11, 1 ( 2010 ), 570. Adrienn Szab\u00f3, \u00c1d\u00e1m Nov\u00e1k, Istv\u00e1n Mikl\u00f3s, and Jotun Hein. 2010. Reticular alignment: A progressive corner-cutting method for multiple sequence alignment. BMC bioinformatics 11, 1 (2010), 570."},{"key":"e_1_3_2_2_31_1","volume-title":"CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research 22, 22","author":"Thompson Julie D","year":"1994","unstructured":"Julie D Thompson , Desmond G Higgins , and Toby J Gibson . 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research 22, 22 ( 1994 ), 4673--4680. Julie D Thompson, Desmond G Higgins, and Toby J Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic acids research 22, 22 (1994), 4673--4680."},{"key":"e_1_3_2_2_32_1","doi-asserted-by":"publisher","DOI":"10.1002\/prot.20527"},{"key":"e_1_3_2_2_33_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0018093"},{"volume-title":"Models and algorithms for genome evolution","author":"Warnow Tandy","key":"e_1_3_2_2_34_1","unstructured":"Tandy Warnow . 2013. Large-scale multiple sequence alignment and phylogeny estimation . In Models and algorithms for genome evolution . Springer , 85--146. Tandy Warnow. 2013. Large-scale multiple sequence alignment and phylogeny estimation. In Models and algorithms for genome evolution. Springer, 85--146."},{"key":"e_1_3_2_2_35_1","volume-title":"Comparing multi-objective metaheuristics for solving a three-objective formulation of multiple sequence alignment. Progress in Artificial Intelligence","author":"Zambrano-Vega Cristian","year":"2017","unstructured":"Cristian Zambrano-Vega , Antonio J Nebro , Jos\u00e9 Garc\u00eda-Nieto , and Jos\u00e9 F Aldana-Montes . 2017. Comparing multi-objective metaheuristics for solving a three-objective formulation of multiple sequence alignment. Progress in Artificial Intelligence ( 2017 ), 1--16. Cristian Zambrano-Vega, Antonio J Nebro, Jos\u00e9 Garc\u00eda-Nieto, and Jos\u00e9 F Aldana-Montes. 2017. Comparing multi-objective metaheuristics for solving a three-objective formulation of multiple sequence alignment. Progress in Artificial Intelligence (2017), 1--16."},{"key":"e_1_3_2_2_36_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx338"},{"key":"e_1_3_2_2_37_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-56154-7_23"}],"event":{"name":"GECCO '19: Genetic and Evolutionary Computation Conference","sponsor":["SIGEVO ACM Special Interest Group on Genetic and Evolutionary Computation"],"location":"Prague Czech Republic","acronym":"GECCO '19"},"container-title":["Proceedings of the Genetic and Evolutionary Computation Conference"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3321707.3321773","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3321707.3321773","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,17]],"date-time":"2025-06-17T23:53:19Z","timestamp":1750204399000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3321707.3321773"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,7,13]]},"references-count":37,"alternative-id":["10.1145\/3321707.3321773","10.1145\/3321707"],"URL":"https:\/\/doi.org\/10.1145\/3321707.3321773","relation":{},"subject":[],"published":{"date-parts":[[2019,7,13]]},"assertion":[{"value":"2019-07-13","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}