G. Cardona, F. Rosselló, and G. Valiente, Comparison of Tree-Child Phylogenetic Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, issue.4, pp.552-569, 2009.
DOI : 10.1109/TCBB.2007.70270

J. M. Chan, G. Carlsson, and R. Rabadan, Topology of viral evolution, Proceedings of the National Academy of Sciences, vol.110, issue.46, pp.18566-18571, 2013.
DOI : 10.1073/pnas.1313480110

T. Dagan, Y. Artzy-randrup, and W. Martin, Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution, Proceedings of the National Academy of Sciences, vol.105, issue.29, pp.10039-10044, 2008.
DOI : 10.1073/pnas.0800679105

D. Gusfield, ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks, 2014.

D. H. Huson, R. Rupp, and C. Scornavacca, Phylogenetic Networks: Concepts, Algorithms and Applications, 2011.
DOI : 10.1017/CBO9780511974076

L. Van-iersel, C. Semple, and M. Steel, Locating a tree in a phylogenetic network, Information Processing Letters, vol.110, issue.23, pp.1037-1043, 2010.
DOI : 10.1016/j.ipl.2010.07.027

P. Jenkins, Y. Song, and R. Brem, Genealogy-Based Methods for Inference of Historical Recombination and Gene Flow and Their Application in Saccharomyces cerevisiae, PLoS ONE, vol.30, issue.11, p.46947, 2012.
DOI : 10.1371/journal.pone.0046947.s006

I. A. Kanj, L. Nakhleh, C. Than, and G. Xia, SEEING THE TREES AND THEIR BRANCHES IN THE NETWORK IS HARD, Theoretical Computer Science, pp.153-164, 2008.
DOI : 10.1142/9789812770998_0011

T. Marcussen, K. S. Jakobsen, J. Danihelka, H. E. Ballard, K. Blaxland et al., Inferring Species Networks from Gene Trees in High-Polyploid North American and Hawaiian Violets (Viola, Violaceae), Systematic Biology, vol.61, issue.1, pp.107-126, 2012.
DOI : 10.1093/sysbio/syr096

K. Mcbreen and P. J. Lockhart, Reconstructing reticulate evolutionary histories of plants, Trends in Plant Science, vol.11, issue.8, pp.103-122, 2006.
DOI : 10.1016/j.tplants.2006.06.004

B. M. Moret, L. Nakhleh, T. Warnow, C. R. Linder, A. Tholse et al., Phylogenetic networks: modeling, reconstructibility, and accuracy, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.1, issue.1, pp.13-23, 2004.
DOI : 10.1109/TCBB.2004.10

L. Nakhleh, Computational approaches to species phylogeny inference and gene tree reconciliation, Trends in Ecology & Evolution, vol.28, issue.12, pp.719-728, 2013.
DOI : 10.1016/j.tree.2013.09.004

L. Parida, Ancestral Recombinations Graph: A Reconstructability Perspective Using Random-Graphs Framework, Journal of Computational Biology, vol.17, issue.10, pp.1345-1370, 2010.
DOI : 10.1089/cmb.2009.0243

T. J. Treangen and E. P. Rocha, Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes, PLoS Genetics, vol.13, issue.1, p.1001284, 2011.
DOI : 10.1371/journal.pgen.1001284.s007
URL : https://hal.archives-ouvertes.fr/pasteur-00578535

L. Wang, K. Zhang, and L. Zhang, Perfect phylogenetic networks with recombination, Proceedings of the 2001 ACM symposium on Applied computing , SAC '01, pp.69-78, 2001.
DOI : 10.1145/372202.372271