{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T00:26:31Z","timestamp":1773275191720,"version":"3.50.1"},"publisher-location":"Cham","reference-count":23,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783030744311","type":"print"},{"value":"9783030744328","type":"electronic"}],"license":[{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2021,1,1]],"date-time":"2021-01-01T00:00:00Z","timestamp":1609459200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021]]},"DOI":"10.1007\/978-3-030-74432-8_12","type":"book-chapter","created":{"date-parts":[[2021,5,30]],"date-time":"2021-05-30T23:02:53Z","timestamp":1622415773000},"page":"159-171","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":4,"title":["The Maximum Weight Trace Alignment Merging Problem"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3550-2636","authenticated-orcid":false,"given":"Paul","family":"Zaharias","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7826-1214","authenticated-orcid":false,"given":"Vladimir","family":"Smirnov","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7717-3514","authenticated-orcid":false,"given":"Tandy","family":"Warnow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2021,5,31]]},"reference":[{"issue":"1","key":"12_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/1471-2105-3-2","volume":"3","author":"JJ Cannone","year":"2002","unstructured":"Cannone, J.J., et al.: The comparative RNA Web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinf. 3(1), 1\u201331 (2002). https:\/\/doi.org\/10.1186\/1471-2105-3-2","journal-title":"BMC Bioinf."},{"issue":"1","key":"12_CR2","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1186\/1471-2105-5-113","volume":"5","author":"RC Edgar","year":"2004","unstructured":"Edgar, R.C.: MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinf. 5(1), 113 (2004)","journal-title":"BMC Bioinf."},{"key":"12_CR3","doi-asserted-by":"crossref","unstructured":"Fiduccia, C.M., Mattheyses, R.M.: A linear-time heuristic for improving network partitions. In: 19th Design Automation Conference, pp. 175\u2013181. IEEE (1982)","DOI":"10.1109\/DAC.1982.1585498"},{"issue":"2","key":"12_CR4","doi-asserted-by":"publisher","first-page":"511","DOI":"10.1093\/nar\/gki198","volume":"33","author":"K Katoh","year":"2005","unstructured":"Katoh, K., Kuma, K.I., Toh, H., Miyata, T.: MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res. 33(2), 511\u2013518 (2005)","journal-title":"Nucleic Acids Res."},{"key":"12_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"106","DOI":"10.1007\/BFb0029800","volume-title":"Combinatorial Pattern Matching","author":"J Kececioglu","year":"1993","unstructured":"Kececioglu, J.: The maximum weight trace problem in multiple sequence alignment. In: Apostolico, A., Crochemore, M., Galil, Z., Manber, U. (eds.) CPM 1993. LNCS, vol. 684, pp. 106\u2013119. Springer, Heidelberg (1993). https:\/\/doi.org\/10.1007\/BFb0029800"},{"issue":"1\u20133","key":"12_CR6","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/S0166-218X(00)00194-3","volume":"104","author":"JD Kececioglu","year":"2000","unstructured":"Kececioglu, J.D., Lenhof, H.P., Mehlhorn, K., Mutzel, P., Reinert, K., Vingron, M.: A polyhedral approach to sequence alignment problems. Discrete Appl. Math. 104(1\u20133), 143\u2013186 (2000)","journal-title":"Discrete Appl. Math."},{"key":"12_CR7","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1007\/978-3-540-30217-9_31","volume-title":"Parallel Problem Solving from Nature - PPSN VIII","author":"G Koller","year":"2004","unstructured":"Koller, G., Raidl, G.R.: An evolutionary algorithm for the maximum weight trace formulation of the multiple sequence alignment problem. In: Yao, X., et al. (eds.) PPSN 2004. LNCS, vol. 3242, pp. 302\u2013311. Springer, Heidelberg (2004). https:\/\/doi.org\/10.1007\/978-3-540-30217-9_31"},{"issue":"1","key":"12_CR8","doi-asserted-by":"publisher","first-page":"48","DOI":"10.1090\/S0002-9939-1956-0078686-7","volume":"7","author":"JB Kruskal","year":"1956","unstructured":"Kruskal, J.B.: On the shortest spanning subtree of a graph and the traveling salesman problem. Proc. Am. Math. Soc. 7(1), 48\u201350 (1956)","journal-title":"Proc. Am. Math. Soc."},{"issue":"5934","key":"12_CR9","doi-asserted-by":"publisher","first-page":"1561","DOI":"10.1126\/science.1171243","volume":"324","author":"K Liu","year":"2009","unstructured":"Liu, K., Raghavan, S., Nelesen, S., Linder, C.R., Warnow, T.: Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324(5934), 1561\u20131564 (2009)","journal-title":"Science"},{"issue":"1","key":"12_CR10","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1093\/sysbio\/syr095","volume":"61","author":"K Liu","year":"2012","unstructured":"Liu, K., et al.: SAT\u00e9-II: very fast and accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Syst. Biol. 61(1), 90 (2012)","journal-title":"Syst. Biol."},{"issue":"5","key":"12_CR11","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1089\/cmb.2014.0156","volume":"22","author":"S Mirarab","year":"2015","unstructured":"Mirarab, S., Nguyen, N., Guo, S., Wang, L.S., Kim, J., Warnow, T.: PASTA: ultra-large multiple sequence alignment for nucleotide and amino-acid sequences. J. Comput. Biol. 22(5), 377\u2013386 (2015)","journal-title":"J. Comput. Biol."},{"issue":"23","key":"12_CR12","doi-asserted-by":"publisher","first-page":"3250","DOI":"10.1093\/bioinformatics\/btr553","volume":"27","author":"S Mirarab","year":"2011","unstructured":"Mirarab, S., Warnow, T.: FASTSP: linear time calculation of alignment accuracy. Bioinformatics 27(23), 3250\u20133258 (2011)","journal-title":"Bioinformatics"},{"issue":"1","key":"12_CR13","first-page":"12","volume":"9","author":"M Modzelewski","year":"2014","unstructured":"Modzelewski, M., Dojer, N.: MSARC: multiple sequence alignment by residue clustering. Alg. Mol. Biol. 9(1), 12 (2014)","journal-title":"Alg. Mol. Biol."},{"issue":"2","key":"12_CR14","doi-asserted-by":"publisher","first-page":"453","DOI":"10.1287\/opre.1120.1139","volume":"61","author":"E Moreno-Centeno","year":"2013","unstructured":"Moreno-Centeno, E., Karp, R.M.: The implicit hitting set approach to solve combinatorial optimization problems with an application to multigenome alignment. Oper. Res. 61(2), 453\u2013468 (2013)","journal-title":"Oper. Res."},{"issue":"1","key":"12_CR15","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1006\/jmbi.2000.4042","volume":"302","author":"C Notredame","year":"2000","unstructured":"Notredame, C., Higgins, D.G., Heringa, J.: T-Coffee: a novel method for fast and accurate multiple sequence alignment. J. Mol. Biol. 302(1), 205\u2013217 (2000)","journal-title":"J. Mol. Biol."},{"key":"12_CR16","doi-asserted-by":"crossref","unstructured":"Reinert, K., Lenhof, H.P., Mutzel, P., Mehlhorn, K., Kececioglu, J.D.: A branch-and-cut algorithm for multiple sequence alignment. In: Proceedings of the First Annual International Conference on Computational Molecular Biology (RECOMB), pp. 241\u2013250 (1997)","DOI":"10.1145\/267521.267845"},{"key":"12_CR17","doi-asserted-by":"crossref","unstructured":"Satuluri, V., Parthasarathy, S.: Scalable graph clustering using stochastic flows: applications to community discovery. In: Proceedings of the 15th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 737\u2013746 (2009)","DOI":"10.1145\/1557019.1557101"},{"key":"12_CR18","doi-asserted-by":"crossref","unstructured":"Smirnov, V., Warnow, T.: MAGUS: multiple sequence alignment using graph clustering. Bioinformatics (2020)","DOI":"10.1093\/bioinformatics\/btaa992"},{"issue":"2","key":"12_CR19","doi-asserted-by":"publisher","first-page":"268","DOI":"10.1093\/sysbio\/syaa058","volume":"70","author":"V Smirnov","year":"2020","unstructured":"Smirnov, V., Warnow, T.: Phylogeny estimation given sequence length heterogeneity. Syst. Biol. 70(2), 268\u2013282 (2020)","journal-title":"Syst. Biol."},{"issue":"2","key":"12_CR20","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1093\/bioinformatics\/14.2.157","volume":"14","author":"J Stoye","year":"1998","unstructured":"Stoye, J., Evers, D., Meyer, F.: Rose: generating sequence families. Bioinformatics 14(2), 157\u2013163 (1998)","journal-title":"Bioinformatics"},{"key":"12_CR21","unstructured":"Van Dongen, S.M.: A cluster algorithm for graphs. Technical report, National Research Institute for Mathematics and Computer Science in the Netherlands, Amsterdam, iNS-R0010, May 2000"},{"key":"12_CR22","doi-asserted-by":"crossref","unstructured":"Wallace, I.M., O\u2019sullivan, O., Higgins, D.G., Notredame, C.: M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34(6), 1692\u20131699 (2006)","DOI":"10.1093\/nar\/gkl091"},{"issue":"13","key":"12_CR23","doi-asserted-by":"publisher","first-page":"i559","DOI":"10.1093\/bioinformatics\/btm226","volume":"23","author":"TJ Wheeler","year":"2007","unstructured":"Wheeler, T.J., Kececioglu, J.D.: Multiple alignment by aligning alignments. Bioinformatics 23(13), i559\u2013i568 (2007)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Algorithms for Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-74432-8_12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,5,30]],"date-time":"2021-05-30T23:03:40Z","timestamp":1622415820000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-74432-8_12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021]]},"ISBN":["9783030744311","9783030744328"],"references-count":23,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-74432-8_12","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021]]},"assertion":[{"value":"31 May 2021","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"AlCoB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Algorithms for Computational Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Missoula, MT","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"USA","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2021","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"7 June 2021","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"11 June 2021","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"8","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"alcob2021","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/irdta.eu\/alcob2020-2021\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"easychair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"22","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"12","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"55% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}