{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T21:38:13Z","timestamp":1773869893854,"version":"3.50.1"},"publisher-location":"Cham","reference-count":33,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783030008338","type":"print"},{"value":"9783030008345","type":"electronic"}],"license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018]]},"DOI":"10.1007\/978-3-030-00834-5_10","type":"book-chapter","created":{"date-parts":[[2018,9,6]],"date-time":"2018-09-06T23:53:16Z","timestamp":1536277996000},"page":"179-195","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":6,"title":["Reconstructing the History of Syntenies Through Super-Reconciliation"],"prefix":"10.1007","author":[{"given":"Matt\u00e9o","family":"Delabre","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nadia","family":"El-Mabrouk","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Katharina T.","family":"Huber","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Manuel","family":"Lafond","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Moulton","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emmanuel","family":"Noutahi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Miguel Sautie","family":"Castellanos","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,9,8]]},"reference":[{"issue":"1","key":"10_CR1","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/1471-2148-7-239","volume":"7","author":"A Abbasi","year":"2007","unstructured":"Abbasi, A., Grzeschik, K.: An insight into the phylogenetic history of hox linked gene families in vertebrates. BMC Evol. Biol. 7(1), 239 (2007)","journal-title":"BMC Evol. Biol."},{"issue":"3","key":"10_CR2","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1137\/0210030","volume":"10","author":"A Aho","year":"1981","unstructured":"Aho, A., Yehoshua, S., Szymanski, T., Ullman, J.: Inferring a tree from lowest common ancestors with an application to the optimization of relational expressions. SIAM J. Comput. 10(3), 405\u2013421 (1981)","journal-title":"SIAM J. Comput."},{"key":"10_CR3","doi-asserted-by":"publisher","first-page":"49","DOI":"10.1016\/j.ympev.2014.09.009","volume":"81","author":"W Ajmal","year":"2014","unstructured":"Ajmal, W., Khan, H., Abbasi, A.: Phylogenetic investigation of human fgfr-bearing paralogons favors piecemeal duplication theory of vertebrate genome evolution. Mol. Phylogenet. Evol. 81, 49\u201360 (2014)","journal-title":"Mol. Phylogenet. Evol."},{"issue":"14","key":"10_CR4","doi-asserted-by":"publisher","first-page":"57145719","DOI":"10.1073\/pnas.0806251106","volume":"106","author":"O Akerborg","year":"2009","unstructured":"Akerborg, O., Sennblad, B., Arvestad, L., Lagergren, J.: Simultaneous bayesian gene tree reconstruction and reconciliation analysis. Proc. Nat. Acad. Sci. USA 106(14), 57145719 (2009)","journal-title":"Proc. Nat. Acad. Sci. USA"},{"issue":"12","key":"10_CR5","doi-asserted-by":"publisher","first-page":"283291","DOI":"10.1093\/bioinformatics\/bts225","volume":"28","author":"M Bansal","year":"2012","unstructured":"Bansal, M., Alm, E., Kellis, M.: Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics 28(12), 283291 (2012). https:\/\/doi.org\/10.1093\/bioinformatics\/bts225","journal-title":"Bioinformatics"},{"issue":"18","key":"10_CR6","doi-asserted-by":"publisher","first-page":"382388","DOI":"10.1093\/bioinformatics\/bts374","volume":"28","author":"S B\u00e9rard","year":"2012","unstructured":"B\u00e9rard, S., Gallien, C., Boussau, B., Szollosi, G., Daubin, V., Tannier, E.: Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics 28(18), 382388 (2012)","journal-title":"Bioinformatics"},{"issue":"3","key":"10_CR7","doi-asserted-by":"publisher","first-page":"225","DOI":"10.1007\/BF00383444","volume":"8","author":"G Brightwell","year":"1991","unstructured":"Brightwell, G., Winkler, P.: Counting linear extensions. Order 8(3), 225\u2013242 (1991)","journal-title":"Order"},{"key":"10_CR8","doi-asserted-by":"publisher","first-page":"101","DOI":"10.1007\/BF01202270","volume":"12","author":"M Constantinescu","year":"1995","unstructured":"Constantinescu, M., Sankoff, D.: An efficient algorithm for supertrees. J. Classif. 12, 101\u2013112 (1995)","journal-title":"J. Classif."},{"key":"10_CR9","doi-asserted-by":"crossref","unstructured":"Dondi, R., Lafond, M., Scornavacca, C.: Reconciling multiple genes trees via segmental duplications and losses. WABI (2018, to appear)","DOI":"10.1186\/s13015-019-0139-6"},{"issue":"5","key":"10_CR10","doi-asserted-by":"publisher","first-page":"392400","DOI":"10.1093\/bib\/bbr045","volume":"12","author":"J Doyon","year":"2011","unstructured":"Doyon, J., Ranwez, V., Daubin, V., Berry, V.: Models, algorithms and programs for phylogeny reconciliation. Briefings Bioinform. 12(5), 392400 (2011)","journal-title":"Briefings Bioinform."},{"issue":"40","key":"10_CR11","doi-asserted-by":"publisher","first-page":"1548715492","DOI":"10.1073\/pnas.0805590105","volume":"105","author":"S Dreborg","year":"2008","unstructured":"Dreborg, S., Sundstrom, G., Larsson, T., Larhammar, D.: Evolution of vertebrate opioid receptors. Proc. Nat. Acad. Sci. USA 105(40), 1548715492 (2008)","journal-title":"Proc. Nat. Acad. Sci. USA"},{"key":"10_CR12","unstructured":"Duchemin, W.: Phylogeny of dependencies and dependencies of phylogenies in genes and genomes. Theses, Universit\u00e9 de Lyon, Dec 2017. https:\/\/tel.archives-ouvertes.fr\/tel-01779517"},{"key":"10_CR13","doi-asserted-by":"crossref","unstructured":"Ferrier, D.: Evolution of homeobox gene clusters in animals:the giga-cluster and primary vs. secondary clustering. Frontiers in Ecology and Evolution 4(34) (2016)","DOI":"10.3389\/fevo.2016.00036"},{"key":"10_CR14","doi-asserted-by":"publisher","first-page":"881892","DOI":"10.1038\/nrg1723","volume":"6","author":"J Garcia-Fern\u00e0ndez","year":"2005","unstructured":"Garcia-Fern\u00e0ndez, J.: The genesis and evolution of homeobox gene clusters. Nat. Rev. Genet. 6, 881892 (2005)","journal-title":"Nat. Rev. Genet."},{"key":"10_CR15","doi-asserted-by":"publisher","first-page":"132","DOI":"10.2307\/2412519","volume":"28","author":"M Goodman","year":"1979","unstructured":"Goodman, M., Czelusniak, J., Moore, G., Romero-Herrera, A., Matsuda, G.: Fitting the gene lineage into its species lineage, a parsimony strategy illustrated by cladograms constructed from globin sequences. Syst. Zool. 28, 132\u2013163 (1979)","journal-title":"Syst. Zool."},{"key":"10_CR16","doi-asserted-by":"publisher","first-page":"95","DOI":"10.1016\/j.ympev.2015.08.019","volume":"94","author":"M Hafeez","year":"2016","unstructured":"Hafeez, M., Shabbir, M., Altaf, F., Abbasi, A.: Phylogenomic analysis reveals ancient segmental duplications in the human genome. Mol. Phylogenet. Evol. 94, 95\u2013100 (2016)","journal-title":"Mol. Phylogenet. Evol."},{"issue":"4","key":"10_CR17","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1137\/0210055","volume":"10","author":"I Holyer","year":"1981","unstructured":"Holyer, I.: The NP-completeness of edge-coloring. SIAM J. Comput. 10(4), 718\u2013720 (1981)","journal-title":"SIAM J. Comput."},{"issue":"22","key":"10_CR18","doi-asserted-by":"publisher","first-page":"4673","DOI":"10.1093\/nar\/22.22.4673","volume":"22","author":"JD Thompson","year":"1994","unstructured":"Thompson, J.D., Higgins, D., Gibson, T.: CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22(22), 4673\u20134680 (1994)","journal-title":"Nucleic Acids Res."},{"issue":"7","key":"10_CR19","doi-asserted-by":"publisher","first-page":"18701874","DOI":"10.1093\/molbev\/msw054","volume":"33","author":"S Kumar","year":"2016","unstructured":"Kumar, S., Stecher, G., Tamura, K.: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33(7), 18701874 (2016)","journal-title":"Mol. Biol. Evol."},{"key":"10_CR20","doi-asserted-by":"crossref","unstructured":"Lafond, M., Ouangraoua, A., El-Mabrouk, N.: Reconstructing a supergenetree minimizing reconciliation. BMC-Genomics 16, S4 (2015). special issue of RECOMB-CG 2015","DOI":"10.1186\/1471-2105-16-S14-S4"},{"key":"10_CR21","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1186\/1471-2148-8-184","volume":"8","author":"T Larsson","year":"2008","unstructured":"Larsson, T., Olsson, F., Sundstrom, G., Lundin, L., Brenner, S., Venkatesh, B., Larhammar, D.: Early vertebrate chromosome duplications and the evolution of the neuropeptide y receptor gene regions. BMC Evol. Biol. 8, 184 (2008)","journal-title":"BMC Evol. Biol."},{"key":"10_CR22","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/0166-218X(95)00074-2","volume":"69","author":"M Ng","year":"1996","unstructured":"Ng, M., Wormald, N.: Reconstruction of rooted trees from subtrees. Discrete Appl. Math 69, 19\u201331 (1996)","journal-title":"Discrete Appl. Math"},{"key":"10_CR23","doi-asserted-by":"crossref","unstructured":"Paszek, J., Gorecki, P.: Efficient algorithms for genomic duplication models. IEEE\/ACM Trans. Comput. Biol. Bioinform. (2017)","DOI":"10.1007\/978-3-319-67979-2_6"},{"issue":"2","key":"10_CR24","doi-asserted-by":"publisher","first-page":"373","DOI":"10.1137\/S0097539791202647","volume":"23","author":"G Pruesse","year":"1994","unstructured":"Pruesse, G., Ruskey, F.: Generating linear extensions fast. SIAM J. Comput. 23(2), 373\u2013386 (1994)","journal-title":"SIAM J. Comput."},{"issue":"3","key":"10_CR25","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1016\/S0166-218X(02)00250-0","volume":"127","author":"C Semple","year":"2003","unstructured":"Semple, C.: Reconstructing minimal rooted trees. Discrete Appl. Math. 127(3), 489\u2013503 (2003)","journal-title":"Discrete Appl. Math."},{"issue":"3","key":"10_CR26","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1093\/sysbio\/syu007","volume":"63","author":"J Sj\u00f6strand","year":"2014","unstructured":"Sj\u00f6strand, J., Tofigh, A., Daubin, V., Arvestad, L., Sennblad, B., Lagergren, J.: A bayesian method for analyzing lateral gene transfer. Syst. Biol. 63(3), 409\u2013420 (2014)","journal-title":"Syst. Biol."},{"key":"10_CR27","first-page":"12471269","volume":"14","author":"C Stevens","year":"2009","unstructured":"Stevens, C.: The evolution of vertebrate opioid receptors. Front. Biosci. J. Virtual Libr. 14, 12471269 (2009)","journal-title":"Front. Biosci. J. Virtual Libr."},{"key":"10_CR28","doi-asserted-by":"crossref","unstructured":"Sundstrom, G., Dreborg, S., Larhammar, D.: Concomitant duplications of opioid peptide and receptor genes before the origin of jawed vertebrates. PLoS ONE 5(5) (2010)","DOI":"10.1371\/journal.pone.0010512"},{"issue":"1","key":"10_CR29","doi-asserted-by":"publisher","first-page":"e42","DOI":"10.1093\/sysbio\/syu048","volume":"64","author":"G Sz\u00f6ll\u0151si","year":"2014","unstructured":"Sz\u00f6ll\u0151si, G., Tannier, E., Daubin, V., Boussau, B.: The inference of gene trees with species trees. Syst. Biol. 64(1), e42\u2013e62 (2014)","journal-title":"Syst. Biol."},{"issue":"2","key":"10_CR30","doi-asserted-by":"publisher","first-page":"517","DOI":"10.1109\/TCBB.2010.14","volume":"8","author":"A Tofigh","year":"2011","unstructured":"Tofigh, A., Hallett, M., Lagergren, J.: Simultaneous identification of duplications and lateral gene transfers. IEEE\/ACM Trans. Comput. BiolBioinform. 8(2), 517\u2013535 (2011). https:\/\/doi.org\/10.1109\/TCBB.2010.14","journal-title":"IEEE\/ACM Trans. Comput. BiolBioinform."},{"issue":"5","key":"10_CR31","doi-asserted-by":"publisher","first-page":"1312","DOI":"10.1093\/gbe\/evx069","volume":"9","author":"W Duchemin","year":"2017","unstructured":"Duchemin, W., et al.: DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies. Genome Biol. Evol. 9(5), 1312\u20131319 (2017)","journal-title":"Genome Biol. Evol."},{"key":"10_CR32","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1089\/cmb.1997.4.177","volume":"4","author":"L Zhang","year":"1997","unstructured":"Zhang, L.: On Mirkin-Muchnik-Smith conjecture for comparing molecular phylogenies. J. Comput. Biol. 4, 177\u2013188 (1997)","journal-title":"J. Comput. Biol."},{"key":"10_CR33","doi-asserted-by":"publisher","first-page":"821","DOI":"10.1093\/bioinformatics\/17.9.821","volume":"17","author":"CM Zmasek","year":"2001","unstructured":"Zmasek, C.M., Eddy, S.R.: A simple algorithm to infer gene duplication and speciiation events on a gene tree. Bioinformatics 17, 821\u2013828 (2001)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Comparative Genomics"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-00834-5_10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,23]],"date-time":"2019-10-23T17:39:51Z","timestamp":1571852391000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-00834-5_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018]]},"ISBN":["9783030008338","9783030008345"],"references-count":33,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-00834-5_10","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018]]}}}