{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,18]],"date-time":"2025-10-18T10:41:19Z","timestamp":1760784079465},"reference-count":16,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2015,11,14]],"date-time":"2015-11-14T00:00:00Z","timestamp":1447459200000},"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":["BMC Bioinformatics"],"published-print":{"date-parts":[[2015,12]]},"DOI":"10.1186\/s12859-015-0803-x","type":"journal-article","created":{"date-parts":[[2015,11,14]],"date-time":"2015-11-14T05:42:49Z","timestamp":1447479769000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":10,"title":["A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality"],"prefix":"10.1186","volume":"16","author":[{"given":"Thu-Hien","family":"To","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Edwin","family":"Jacox","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vincent","family":"Ranwez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Celine","family":"Scornavacca","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2015,11,14]]},"reference":[{"key":"803_CR1","volume-title":"Research in Computational Molecular Biology: Proceedings of the 14th International Conference on Research in Computational Molecular Biology (RECOMB). LNCS. vol. 6398","author":"JP Doyon","year":"2010","unstructured":"Doyon JP, Scornavacca C, Gorbunov KY, Sz\u00f6llo\u030bsi GJ, Ranwez V, Berry V. An efficient algorithm for gene\/species trees parsimonious reconciliation with losses, duplications and transfers. In: Research in Computational Molecular Biology: Proceedings of the 14th International Conference on Research in Computational Molecular Biology (RECOMB). LNCS. vol. 6398. Berlin\/Heidelberg, Germany: Springer: 2010. p. 93\u2013108. Software downloadable at http:\/\/www.atgc-montpellier.fr\/Mowgli\/ ."},{"key":"803_CR2","doi-asserted-by":"publisher","first-page":"946","DOI":"10.1134\/S0026893309060053","volume":"43","author":"KY Gorbunov","year":"2009","unstructured":"Gorbunov KY, Lyubetsky VA. Reconstructing genes evolution along a species tree. Mol Biol (Mosk). 2009; 43:946\u201358.","journal-title":"Mol Biol (Mosk)"},{"key":"803_CR3","unstructured":"Tofigh A. Using trees to capture reticulate evolution, lateral gene transfers and cancer progression. PhD thesis, KTH Royal Institute of Technology, Sweden. 2009."},{"key":"803_CR4","doi-asserted-by":"crossref","unstructured":"Tofigh A, Hallett MT, Lagergren J. Simultaneous identification of duplications and lateral gene transfers. IEEE\/ACM Trans Comput Biology Bioinform. 2011:517\u2013535.","DOI":"10.1109\/TCBB.2010.14"},{"issue":"1","key":"803_CR5","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1089\/cmb.2009.0240","volume":"18","author":"Y Ovadia","year":"2011","unstructured":"Ovadia Y, Fielder D, Conow C, Libeskind-Hadas R. The cophylogeny reconstruction problem is NP-complete. J Comput Bio. 2011; 18(1):59\u201365.","journal-title":"J Comput Bio"},{"issue":"1","key":"803_CR6","first-page":"105","volume":"16","author":"R Libeskind-Hadas","year":"2009","unstructured":"Libeskind-Hadas R, Charleston MA. On the computational complexity of the reticulate cophylogeny reconstruction problem. JCB. 2009; 16(1):105\u201317.","journal-title":"JCB"},{"key":"803_CR7","doi-asserted-by":"crossref","unstructured":"Scornavacca C, Paprotny W, Berry V, Ranwez V. Representing a set of reconciliations in a compact way. J Bioinforma Comput Biol. 2013; 11(2).","DOI":"10.1142\/S0219720012500254"},{"issue":"10","key":"803_CR8","doi-asserted-by":"publisher","first-page":"73667","DOI":"10.1371\/journal.pone.0073667","volume":"8","author":"TH Nguyen","year":"2013","unstructured":"Nguyen TH, Ranwez V, Berry V, Scornavacca C. Support measures to estimate the reliability of evolutionary events predicted by reconciliation methods. PLoS ONE. 2013; 8(10):73667.","journal-title":"PLoS ONE"},{"key":"803_CR9","volume-title":"Proceedings of the 17th International Conference on Research in Computational Molecular Biology. RECOMB\u201913","author":"MS Bansal","year":"2013","unstructured":"Bansal MS, Alm EJ, Kellis M. Reconciliation revisited: Handling multiple optima when reconciling with duplication, transfer, and loss. In: Proceedings of the 17th International Conference on Research in Computational Molecular Biology. RECOMB\u201913. Berlin, Heidelberg: Springer: 2013. p. 1\u201313."},{"issue":"12","key":"803_CR10","doi-asserted-by":"publisher","first-page":"87","DOI":"10.1093\/bioinformatics\/btu289","volume":"30","author":"R Libeskind-Hadas","year":"2014","unstructured":"Libeskind-Hadas R, Wu YC, Bansal MS, Kellis M. Pareto-optimal phylogenetic tree reconciliation. Bioinformatics. 2014; 30(12):87\u201395.","journal-title":"Bioinformatics"},{"issue":"12","key":"803_CR11","doi-asserted-by":"publisher","first-page":"283","DOI":"10.1093\/bioinformatics\/bts225","volume":"28","author":"MS Bansal","year":"2012","unstructured":"Bansal MS, Alm EJ, Kellis M. Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss. Bioinformatics. 2012; 28(12):283\u201391.","journal-title":"Bioinformatics"},{"issue":"1","key":"803_CR12","doi-asserted-by":"publisher","first-page":"12","DOI":"10.1186\/1748-7188-8-12","volume":"8","author":"TH Nguyen","year":"2013","unstructured":"Nguyen TH, Ranwez V, Pointet S, Chifolleau AM, Doyon JP, Berry V. Reconciliation and local gene tree rearrangement can be of mutual profit. Algorithms Mol Biol. 2013; 8(1):12.","journal-title":"Algorithms Mol Biol"},{"key":"803_CR13","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1038\/nature09649","volume":"469","author":"LA David","year":"2011","unstructured":"David LA, Alm EJ. Rapid evolutionary innovation during an archaean genetic expansion. Nature. 2011; 469:93\u20136.","journal-title":"Nature"},{"issue":"3","key":"803_CR14","doi-asserted-by":"publisher","first-page":"235","DOI":"10.1093\/bioinformatics\/13.3.235","volume":"13","author":"A Rambaut","year":"1997","unstructured":"Rambaut A, Grass NC. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Bioinformatics. 1997; 13(3):235\u20138.","journal-title":"Bioinformatics"},{"issue":"21","key":"803_CR15","doi-asserted-by":"publisher","first-page":"2688","DOI":"10.1093\/bioinformatics\/btl446","volume":"22","author":"A Stamatakis","year":"2006","unstructured":"Stamatakis A. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics. 2006; 22(21):2688\u2013690.","journal-title":"Bioinformatics"},{"key":"803_CR16","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1186\/1748-7188-5-16","volume":"5","author":"C Conow","year":"2010","unstructured":"Conow C, Fielder D, Ovadia Y, Libeskind-Hadas R. Jane: a new tool for the cophylogeny reconstruction problem. Algorithms Mol Biol. 2010; 5:16. Software downloadable at http:\/\/www.cs.hmc.edu\/~hadas\/jane\/ .","journal-title":"Algorithms Mol Biol"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0803-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12859-015-0803-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-015-0803-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,1]],"date-time":"2019-09-01T14:55:19Z","timestamp":1567349719000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-015-0803-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015,11,14]]},"references-count":16,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2015,12]]}},"alternative-id":["803"],"URL":"https:\/\/doi.org\/10.1186\/s12859-015-0803-x","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,11,14]]},"article-number":"384"}}