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

L. Nakhleh, Evolutionary Phylogenetic Networks: Models and Issues, The Problem Solving Handbook in Computational Biology and Bioinformatics, pp.125-158, 2011.
DOI : 10.1007/978-0-387-09760-2_7

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.215.3536

D. Morrison, Introduction to Phylogenetic Networks, 2011.

A. Nolte and D. Tautz, Understanding the onset of hybrid speciation, Trends in Genetics, vol.26, issue.2, pp.54-58, 2010.
DOI : 10.1016/j.tig.2009.12.001

H. Ochman, J. Lawrence, and E. Groisman, Lateral gene transfer and the nature of bacterial innovation, Nature, vol.405, issue.6784, pp.299-304, 2000.
DOI : 10.1038/35012500

L. Boto, Horizontal gene transfer in evolution: facts and challenges, Proceedings of the Royal Society B: Biological Sciences, vol.8, issue.2, pp.819-827, 2010.
DOI : 10.1016/0022-5193(65)90083-4

G. Smith, D. Vijaykrishna, J. Bahl, S. Lycett, and M. Worobey, Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic, Nature, vol.22, issue.7250, pp.1122-1125, 2009.
DOI : 10.1038/nature08182

A. Rambaut, D. Posada, K. Crandall, and E. Holmes, The causes and consequences of HIV evolution, Nature Reviews Genetics, vol.5, issue.1, pp.52-61, 2004.
DOI : 10.1038/nrg1246

E. Simon-loriere and E. Holmes, Why do RNA viruses recombine?, Nature Reviews Microbiology, vol.23, issue.8, pp.617-626, 2011.
DOI : 10.1038/nrmicro2614

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3324781

Y. Song and J. Hein, Constructing Minimal Ancestral Recombination Graphs, Journal of Computational Biology, vol.12, issue.2, pp.147-169, 2005.
DOI : 10.1089/cmb.2005.12.147

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.85.964

M. Minichiello and R. Durbin, Mapping Trait Loci by Use of Inferred Ancestral Recombination Graphs, The American Journal of Human Genetics, vol.79, issue.5, pp.910-922, 2006.
DOI : 10.1086/508901

M. Rasmussen, M. Hubisz, I. Gronau, and A. Siepel, Genome-Wide Inference of Ancestral Recombination Graphs, PLoS Genetics, vol.45, issue.2, p.1004342, 2014.
DOI : 10.1371/journal.pgen.1004342.s022

D. Huson and D. Bryant, Application of Phylogenetic Networks in Evolutionary Studies, Molecular Biology and Evolution, vol.23, issue.2, pp.254-267, 2006.
DOI : 10.1093/molbev/msj030

D. Bryant and V. Moulton, Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks, Molecular Biology and Evolution, vol.21, issue.2, pp.255-265, 2004.
DOI : 10.1093/molbev/msh018

G. Jin, L. Nakhleh, S. Snir, and T. Tuller, Maximum likelihood of phylogenetic networks, Bioinformatics, vol.22, issue.21, pp.2604-2611, 2006.
DOI : 10.1093/bioinformatics/btl452

H. Park and L. Nakhleh, Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria, BMC Bioinformatics, vol.13, p.12, 2012.

L. Van-iersel, S. Kelk, R. Rupp, and D. Huson, Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters, Proceedings of the 18th Annual International Conference on Intelligent Systems for Molecular Biology, pp.124-131, 2010.
DOI : 10.1093/bioinformatics/btq202

T. To and M. Habib, Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time, Combinatorial Pattern Matching: Proceeding of the 20th Annual Symposium Combinatorial Pattern Matching (CPM), pp.275-288, 2009.
DOI : 10.1007/978-3-540-78839-3_40

S. Grünewald, K. Forslund, A. Dress, and V. Moulton, QNet: An Agglomerative Method for the Construction of Phylogenetic Networks from Weighted Quartets, Molecular Biology and Evolution, vol.24, issue.2, pp.532-538, 2007.
DOI : 10.1093/molbev/msl180

M. Baroni, C. Semple, and M. Steel, Hybrids in Real Time, Systematic Biology, vol.55, issue.1, pp.46-56, 2006.
DOI : 10.1080/10635150500431197

Y. Yu, J. Degnan, and L. Nakhleh, The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection, PLoS Genetics, vol.8, issue.4, p.1002660, 2012.
DOI : 10.1371/journal.pgen.1002660.s001

R. Radice, A Bayesian Approach to Phylogenetic Networks, 2011.

D. Gusfield, S. Eddhu, and C. Langley, Efficient reconstruction of phylogenetic networks with constrained recombinations, Proceedings of the IEEE Computer Society Conference on Bioinformatics (CSB), p.363, 2003.

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

D. Huson, R. Rupp, V. Berry, P. Gambette, and C. Paul, Computing galled networks from real data, Bioinformatics, vol.25, issue.12, pp.85-93, 2009.
DOI : 10.1093/bioinformatics/btp217

URL : https://hal.archives-ouvertes.fr/lirmm-00368545

C. Choy, J. Jansson, K. Sadakane, and W. Sung, Computing the maximum agreement of phylogenetic networks, Theoretical Computer Science, vol.335, issue.1, pp.93-107, 2005.
DOI : 10.1016/j.tcs.2004.12.012

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, 2007.
DOI : 10.1109/TCBB.2007.70270

G. Cardona, M. Llabrés, F. Rosselló, and G. Valiente, A distance metric for a class of tree-sibling phylogenetic networks, Bioinformatics, vol.24, issue.13, pp.1481-1488, 2008.
DOI : 10.1093/bioinformatics/btn231

B. Moret, L. Nakhleh, T. Warnow, C. Linder, and A. Tholse, 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, A Metric on the Space of Reduced Phylogenetic Networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.7, issue.2, pp.218-222, 2010.
DOI : 10.1109/TCBB.2009.2

M. Baroni, C. Semple, and M. Steel, A Framework for Representing Reticulate Evolution, Annals of Combinatorics, vol.8, issue.4, pp.391-408, 2004.
DOI : 10.1007/s00026-004-0228-0