{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,1]],"date-time":"2026-01-01T03:09:02Z","timestamp":1767236942213,"version":"3.40.3"},"publisher-location":"Cham","reference-count":25,"publisher":"Springer Nature Switzerland","isbn-type":[{"type":"print","value":"9783031580710"},{"type":"electronic","value":"9783031580727"}],"license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024]]},"DOI":"10.1007\/978-3-031-58072-7_3","type":"book-chapter","created":{"date-parts":[[2024,4,14]],"date-time":"2024-04-14T19:01:42Z","timestamp":1713121302000},"page":"47-68","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Inferring Transcript Phylogenies from\u00a0Transcript Ortholog Clusters"],"prefix":"10.1007","author":[{"given":"Wend Yam D. D.","family":"Ouedraogo","sequence":"first","affiliation":[]},{"given":"Aida","family":"Ouangraoua","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2024,4,15]]},"reference":[{"key":"3_CR1","doi-asserted-by":"crossref","unstructured":"Adami, C., Ofria, C., Collier, T.C.: Evolution of biological complexity. Proc. Natl. Acad. Sci. 97(9), 4463\u20134468 (2000)","DOI":"10.1073\/pnas.97.9.4463"},{"key":"3_CR2","doi-asserted-by":"crossref","unstructured":"Ait-Hamlat, A., Zea, D.J., Labeeuw, A., Polit, L., Richard, H., Laine, E.: Transcripts\u2019 evolutionary history and structural dynamics give mechanistic insights into the functional diversity of the jnk family. J. Mol. Biol. 432(7), 2121\u20132140 (2020)","DOI":"10.1016\/j.jmb.2020.01.032"},{"key":"3_CR3","doi-asserted-by":"crossref","unstructured":"Ara\u00fajo, G.S., Telles, G.P., Walter, M.E.M., Almeida, N.F.: Distance-based live phylogeny. In: International Conference on Bioinformatics Models, Methods and Algorithms, vol. 4, pp. 196\u2013201. SCITEPRESS (2017)","DOI":"10.5220\/0006224501960201"},{"key":"3_CR4","doi-asserted-by":"crossref","unstructured":"Black, D.L.: Protein diversity from alternative splicing: a challenge for bioinformatics and post-genome biology. Cell 103(3), 367\u2013370 (2000)","DOI":"10.1016\/S0092-8674(00)00128-8"},{"key":"3_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1007\/978-3-642-02008-7_4","volume-title":"Research in Computational Molecular Biology","author":"C Chauve","year":"2009","unstructured":"Chauve, C., El-Mabrouk, N.: New perspectives on gene family evolution: losses in reconciliation and a link with supertrees. In: Batzoglou, S. (ed.) RECOMB 2009. LNCS, vol. 5541, pp. 46\u201358. Springer, Heidelberg (2009). https:\/\/doi.org\/10.1007\/978-3-642-02008-7_4"},{"issue":"9","key":"3_CR6","doi-asserted-by":"publisher","first-page":"S1","DOI":"10.1186\/1471-2105-13-S9-S1","volume":"13","author":"Y Christinat","year":"2012","unstructured":"Christinat, Y., Moret, B.M.E.: Inferring transcript phylogenies. BMC Bioinformatics 13(9), S1 (2012)","journal-title":"BMC Bioinformatics"},{"issue":"6","key":"3_CR7","doi-asserted-by":"publisher","first-page":"1403","DOI":"10.1109\/TCBB.2012.145","volume":"10","author":"Y Christinat","year":"2013","unstructured":"Christinat, Y., Moret, B.M.E.: A transcript perspective on evolution. IEEE\/ACM Trans. Comput. Biol. Bioinf. 10(6), 1403\u20131411 (2013)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"issue":"3","key":"3_CR8","doi-asserted-by":"publisher","first-page":"587","DOI":"10.1093\/molbev\/msh049","volume":"21","author":"R Desper","year":"2004","unstructured":"Desper, R., Gascuel, O.: Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol. Biol. Evol. 21(3), 587\u2013598 (2004)","journal-title":"Mol. Biol. Evol."},{"key":"3_CR9","doi-asserted-by":"crossref","unstructured":"Gascuel, O.: Mathematics of Evolution and Phylogeny. OUP Oxford, Oxford (2005)","DOI":"10.1093\/oso\/9780198566106.001.0001"},{"key":"3_CR10","series-title":"Methods in Molecular Biology","doi-asserted-by":"publisher","first-page":"241","DOI":"10.1007\/978-1-0716-1036-7_15","volume-title":"Multiple Sequence Alignment","author":"M Gouy","year":"2021","unstructured":"Gouy, M., Tannier, E., Comte, N., Parsons, D.P.: Seaview version 5: a multiplatform software for multiple sequence alignment, molecular phylogenetic analyses, and tree reconciliation. In: Katoh, K. (ed.) Multiple Sequence Alignment. MMB, vol. 2231, pp. 241\u2013260. Springer, New York (2021). https:\/\/doi.org\/10.1007\/978-1-0716-1036-7_15"},{"issue":"9","key":"3_CR11","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1101\/gr.135350.111","volume":"22","author":"J Harrow","year":"2012","unstructured":"Harrow, J., et al.: Gencode: the reference human genome annotation for the encode project. Genome Res. 22(9), 1760\u20131774 (2012)","journal-title":"Genome Res."},{"key":"3_CR12","unstructured":"Kidd, K.K., Sgaramella-Zonta, L.A.: Phylogenetic analysis: concepts and methods. Am. J. Hum. Genet. 23(3), 235 (1971)"},{"issue":"20","key":"3_CR13","doi-asserted-by":"publisher","first-page":"640","DOI":"10.1186\/s12859-019-3207-5","volume":"20","author":"E Kuitche","year":"2019","unstructured":"Kuitche, E., Jammali, S., Ouangraoua, A.: Simspliceevol: alternative splicing-aware simulation of biological sequence evolution. BMC Bioinformatics 20(20), 640 (2019)","journal-title":"BMC Bioinformatics"},{"issue":"06","key":"3_CR14","doi-asserted-by":"publisher","first-page":"1740007","DOI":"10.1142\/S0219720017400078","volume":"15","author":"E Kuitche","year":"2017","unstructured":"Kuitche, E., Lafond, M., Ouangraoua, A.: Reconstructing protein and gene phylogenies using reconciliation and soft-clustering. J. Bioinform. Comput. Biol. 15(06), 1740007 (2017)","journal-title":"J. Bioinform. Comput. Biol."},{"issue":"5","key":"3_CR15","doi-asserted-by":"publisher","first-page":"1560","DOI":"10.1109\/TCBB.2017.2720581","volume":"15","author":"M Lafond","year":"2017","unstructured":"Lafond, M., Chauve, C., El-Mabrouk, N., Ouangraoua, A.: Gene tree construction and correction using supertree and reconciliation. IEEE\/ACM Trans. Comput. Biol. Bioinf. 15(5), 1560\u20131570 (2017)","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinf."},{"key":"3_CR16","doi-asserted-by":"publisher","unstructured":"Ouedraogo, W.Y.D.D., Ouangraoua, A.: Inferring clusters of orthologous and paralogous transcripts. In: Jahn, K., Vinar, T. (eds.) Comparative Genomics. RECOMB-CG 2023. LNCS, vol. 13883, pp. 19\u201334. Springer, Cham (2023). https:\/\/doi.org\/10.1007\/978-3-031-36911-7_2","DOI":"10.1007\/978-3-031-36911-7_2"},{"key":"3_CR17","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1007\/s002390010065","volume":"51","author":"Y Pauplin","year":"2000","unstructured":"Pauplin, Y.: Direct calculation of a tree length using a distance matrix. J. Mol. Evol. 51, 41\u201347 (2000)","journal-title":"J. Mol. Evol."},{"key":"3_CR18","doi-asserted-by":"crossref","unstructured":"Ranwez, V., Douzery, E.J., Cambon, C., Chantret, N., Delsuc, F.: MACSE V2: toolkit for the alignment of coding sequences accounting for frameshifts and stop codons. Mol. Biol. Evol. 35(10), 2582\u20132584 (2018)","DOI":"10.1093\/molbev\/msy159"},{"issue":"5","key":"3_CR19","first-page":"1073","volume":"10","author":"A Rzhetsky","year":"1993","unstructured":"Rzhetsky, A., Nei, M.: Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol. Biol. Evol. 10(5), 1073\u20131095 (1993)","journal-title":"Mol. Biol. Evol."},{"issue":"4","key":"3_CR20","first-page":"406","volume":"4","author":"N Saitou","year":"1987","unstructured":"Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4(4), 406\u2013425 (1987)","journal-title":"Mol. Biol. Evol."},{"key":"3_CR21","doi-asserted-by":"crossref","unstructured":"Szollosi, G.J., Tannier, E., Daubin, V., Boussau, B.: The inference of gene trees with species trees. Syst. Biol. 64(1), e42\u2013e62 (2015)","DOI":"10.1093\/sysbio\/syu048"},{"key":"3_CR22","doi-asserted-by":"crossref","unstructured":"Telles, G.P., Almeida, N.F., Minghim, R., Walter, M.E.M.: Live phylogeny. J. Comput. Biol. 20(1), 30\u201337 (2013)","DOI":"10.1089\/cmb.2012.0219"},{"key":"3_CR23","doi-asserted-by":"crossref","unstructured":"Thomas, P.D.: GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics 11(1), 1\u201319 (2010)","DOI":"10.1186\/1471-2105-11-312"},{"key":"3_CR24","doi-asserted-by":"crossref","unstructured":"Zea, D.J., Laskina, S., Baudin, A., Richard, H., Laine, E.: Assessing conservation of alternative splicing with evolutionary splicing graphs. Genome Res. 31(8), 1462\u20131473 (2021)","DOI":"10.1101\/gr.274696.120"},{"key":"3_CR25","doi-asserted-by":"crossref","unstructured":"Zerbino, D.R., et\u00a0al.: Ensembl 2018. Nucl. Acids Res. 46(D1), D754\u2013D761 (2018)","DOI":"10.1093\/nar\/gkx1098"}],"container-title":["Lecture Notes in Computer Science","Comparative Genomics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-031-58072-7_3","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,10,14]],"date-time":"2024-10-14T13:02:24Z","timestamp":1728910944000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-58072-7_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024]]},"ISBN":["9783031580710","9783031580727"],"references-count":25,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-58072-7_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2024]]},"assertion":[{"value":"15 April 2024","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"RECOMB-CG","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"RECOMB International Workshop on Comparative Genomics","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Boston, MA","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":"2024","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"27 April 2024","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"28 April 2024","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"21","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"rcg2024","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}