/. Berlin and . Heidelberg, Software downloadable at http://www.atgc-montpellier, pp.93-108, 2010.

K. Gorbunov and V. Lyubetsky, Reconstructing the evolution of genes along the species tree, Molecular Biology, vol.43, issue.5, pp.946-58, 2009.
DOI : 10.1134/S0026893309050197

A. Tofigh, Using trees to capture reticulate evolution, lateral gene transfers and cancer progression, 2009.

A. Tofigh, M. Hallett, and J. Lagergren, 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

Y. Ovadia, D. Fielder, C. Conow, and R. Libeskind-hadas, 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

R. Libeskind-hadas and M. Charleston, 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

C. Scornavacca, W. Paprotny, V. Berry, and V. Ranwez, 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

T. Nguyen, V. Ranwez, V. Berry, and C. Scornavacca, 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

M. Bansal, E. Alm, and M. Kellis, 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

R. Libeskind-hadas, Y. Wu, M. Bansal, and M. Kellis, 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

M. Bansal, E. Alm, and M. Kellis, 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

T. Nguyen, V. Ranwez, S. Pointet, A. Chifolleau, J. Doyon et al., 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

L. David and E. Alm, Rapid evolutionary innovation during an Archaean genetic expansion, Nature, vol.15, issue.7328, pp.93-99, 2011.
DOI : 10.1101/gr.3844805

A. Rambaut and N. Grass, 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

A. Stamatakis, 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

C. Conow, D. Fielder, Y. Ovadia, and R. Libeskind-hadas, 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