M. S. Bansal, E. J. Alm, and M. Kellis, Efficient algorithms for the reconciliation problem with gene duplication, horizontal transfer and loss, Bioinformatics, vol.28, issue.12, pp.283-291, 2012.
DOI : 10.1093/bioinformatics/bts225

C. Baudet, B. Donati, B. Sinaimeri, P. Crescenzi, C. Gautier et al., Cophylogeny Reconstruction via an Approximate Bayesian Computation, Systematic Biology, vol.64, issue.3, pp.416-431, 2015.
DOI : 10.1093/sysbio/syu129
URL : https://hal.archives-ouvertes.fr/hal-01092972

M. A. Charleston, Jungles: a new solution to the host/parasite phylogeny reconciliation problem, Mathematical Biosciences, vol.149, issue.2, pp.191-223, 1998.
DOI : 10.1016/S0025-5564(97)10012-8

M. A. Charleston, Recent Results in Cophylogeny Mapping, Adv. Parasitol, vol.54, pp.303-330, 2003.
DOI : 10.1016/S0065-308X(03)54007-6

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, pp.1-10, 2010.
DOI : 10.1186/1748-7188-5-16

B. Donati, C. Baudet, B. Sinaimeri, P. Crescenzi, and M. Sagot, EUCALYPT: efficient tree reconciliation enumerator, Algorithms for Molecular Biology, vol.10, issue.1, p.3, 2014.
DOI : 10.1111/j.1755-0998.2010.02955.x
URL : https://hal.archives-ouvertes.fr/hal-01147024

J. Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szöll?-osi, V. Ranwez et al., An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, Proceedings of the 8th annual RECOMB Satellite Workshop on Comparative Genomics (RECOMB-CG 2010), volume 6398 of LNB, pp.93-108, 2011.
DOI : 10.1007/978-3-642-16181-0_9
URL : https://hal.archives-ouvertes.fr/lirmm-00818889

P. Górecki, O. Eulenstein, and J. Tiuryn, Unrooted Tree Reconciliation: A Unified Approach, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, issue.2, pp.522-536, 2013.
DOI : 10.1109/TCBB.2013.22

B. Holland, D. Penny, and M. Hendy, Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock--A Simulation Study, Systematic Biology, vol.52, issue.2, pp.229-238, 2003.
DOI : 10.1080/10635150390192771

S. Keller-schmidt, N. Wieseke, K. Klemm, and M. Middendorf, Evaluation of host parasite reconciliation methods using a new approach for cophylogeny generation, 2011.

W. A. Kosters and J. F. Laros, Metrics for Mining Multisets, Research and Development in Intelligent Systems XXIV, pp.293-303, 2008.
DOI : 10.1007/978-1-84800-094-0_22

D. Merkle and M. Middendorf, Reconstruction of the cophylogenetic history of related phylogenetic trees with divergence timing information, Theory in Biosciences, vol.123, issue.4, pp.277-299, 2005.
DOI : 10.1016/j.thbio.2005.01.003

D. Merkle, M. Middendorf, and N. Wieseke, A parameter-adaptive dynamic programming approach for inferring cophylogenies, BMC Bioinformatics, vol.11, issue.Suppl 1, p.60, 2010.
DOI : 10.1186/1471-2105-11-S1-S60

M. Nei and S. Kumar, Molecular evolution and phylogenetics, 2000.

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

R. D. Page, PARALLEL PHYLOGENIES: RECONSTRUCTING THE HISTORY OF HOST-PARASITE ASSEMBLAGES, Cladistics, vol.37, issue.2, pp.155-173, 1994.
DOI : 10.1016/0020-7519(93)90041-V

A. M. Paterson, R. D. Gray, D. H. Clayton, and J. Moore, Host-parasite co-speciation, host switching, and missing the boat, Host-parasite evolution: general principles and avian models, pp.236-250, 1997.

Y. Qiu, J. Lee, B. A. Whitlock, F. Bernasconi-quadroni, and O. Dombrovska, Was the ANITA Rooting of the Angiosperm Phylogeny Affected by Long-Branch Attraction?, Molecular Biology and Evolution, vol.18, issue.9, pp.1745-1753, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003962

M. J. Sanderson and H. B. Shaffer, Troubleshooting Molecular Phylogenetic Analyses, Annual Review of Ecology and Systematics, vol.33, issue.1, pp.49-72, 2002.
DOI : 10.1146/annurev.ecolsys.33.010802.150509

J. Stavrinides and D. S. Guttman, Mosaic Evolution of the Severe Acute Respiratory Syndrome Coronavirus, Journal of Virology, vol.78, issue.1, pp.76-82, 2004.
DOI : 10.1128/JVI.78.1.76-82.2004

M. Stolzer, H. Lai, M. Xu, D. Sathaye, B. Vernot et al., Inferring duplications, losses, transfers and incomplete lineage sorting with nonbinary species trees, Bioinformatics, vol.28, issue.18, pp.409-415, 2012.
DOI : 10.1093/bioinformatics/bts386

D. L. Swofford, G. J. Olsen, P. J. Waddell, and D. M. Hillis, Phylogenetic inference, Molecular systematics, pp.407-514, 1996.

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.517-535, 2011.
DOI : 10.1109/TCBB.2010.14