Software downloadable at http://www.atgc-montpellier, pp.93-108, 2010. ,
Reconstructing the evolution of genes along the species tree, Molecular Biology, vol.43, issue.5, pp.946-58, 2009. ,
DOI : 10.1134/S0026893309050197
Using trees to capture reticulate evolution, lateral gene transfers and cancer progression, 2009. ,
Simultaneous Identification of Duplications and Lateral Gene Transfers, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, issue.2, pp.2011517-535 ,
DOI : 10.1109/TCBB.2010.14
URL : http://kth.diva-portal.org/smash/get/diva2:233570/FULLTEXT01
The Cophylogeny Reconstruction Problem Is NP-Complete, Journal of Computational Biology, vol.18, issue.1, pp.59-65, 2011. ,
DOI : 10.1089/cmb.2009.0240
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.369.7404
On the Computational Complexity of the Reticulate Cophylogeny Reconstruction Problem, Journal of Computational Biology, vol.16, issue.1, pp.105-122, 2009. ,
DOI : 10.1089/cmb.2008.0084
REPRESENTING A SET OF RECONCILIATIONS IN A COMPACT WAY, Journal of Bioinformatics and Computational Biology, vol.11, issue.02, 2013. ,
DOI : 10.1093/bioinformatics/btq675
URL : https://hal.archives-ouvertes.fr/lirmm-00818801
Support Measures to Estimate the Reliability of Evolutionary Events Predicted by Reconciliation Methods, PLoS ONE, vol.93, issue.10, p.73667, 2013. ,
DOI : 10.1371/journal.pone.0073667.s001
URL : https://hal.archives-ouvertes.fr/hal-01189798
Reconciliation revisited: Handling multiple optima when reconciling with duplication, transfer, and loss, Proceedings of the 17th International Conference on Research in Computational Molecular Biology. RECOMB'13, pp.1-13, 2013. ,
DOI : 10.1089/cmb.2013.0073
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791060
Pareto-optimal phylogenetic tree reconciliation, Bioinformatics, vol.30, issue.12, pp.87-95, 2014. ,
DOI : 10.1093/bioinformatics/btu289
URL : https://academic.oup.com/bioinformatics/article-pdf/30/12/i87/17347240/btu289.pdf
Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.28, issue.12, pp.283-91, 2012. ,
DOI : 10.1093/bioinformatics/bts225
Reconciliation and local gene tree rearrangement can be of mutual profit, Algorithms for Molecular Biology, vol.8, issue.1, p.12, 2013. ,
DOI : 10.1073/pnas.1202997109
URL : https://hal.archives-ouvertes.fr/lirmm-00812726
Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.15, issue.7328, pp.93-99, 2011. ,
DOI : 10.1101/gr.3844805
Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Bioinformatics, vol.13, issue.3, pp.235-243, 1997. ,
DOI : 10.1093/bioinformatics/13.3.235
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-690, 2006. ,
DOI : 10.1093/bioinformatics/btl446
Jane: a new tool for the cophylogeny reconstruction problem, Algorithms for Molecular Biology, vol.5, issue.1, p.16, 2010. ,
DOI : 10.1186/1748-7188-5-16