R. Abbott, D. Albach, S. Ansell, J. Arntzen, S. Baird et al., Hybridization and speciation, Journal of Evolutionary Biology, vol.9, issue.2, pp.229-246, 2013.
DOI : 10.1111/j.1420-9101.2012.02599.x

E. Bapteste, L. Van-iersel, A. Janke, S. Kelchner, S. Kelk et al., Networks: expanding evolutionary thinking, Trends in Genetics, vol.29, issue.8, pp.439-441, 2013.
DOI : 10.1016/j.tig.2013.05.007

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

M. Bordewich and N. Tokac, An algorithm for reconstructing ultrametric tree-child networks from inter-taxa distances, Discrete Applied Mathematics, vol.213, 2016.
DOI : 10.1016/j.dam.2016.05.011

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, 1683.
DOI : 10.1016/0022-5193(65)90083-4

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

H. L. Chan, J. Jansson, T. W. Lam, and S. M. Yiu, RECONSTRUCTING AN ULTRAMETRIC GALLED PHYLOGENETIC NETWORK FROM A DISTANCE MATRIX, Journal of Bioinformatics and Computational Biology, vol.04, issue.04, pp.807-832, 2006.
DOI : 10.1142/S0219720006002211

C. Choy, J. Jansson, K. Sadakane, and W. K. 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

P. Cordue, S. Linz, and C. Semple, Phylogenetic Networks that Display a Tree Twice, Bulletin of Mathematical Biology, vol.7, issue.10, pp.2664-2679, 2014.
DOI : 10.1007/s11538-014-0032-x

T. H. Cormen, C. E. Leiserson, R. L. Rivest, and C. Stein, Introduction to algorithms, 2001.

W. F. Doolittle, Phylogenetic Classification and the Universal Tree, Science, vol.284, issue.5423, pp.2124-2128, 1999.
DOI : 10.1126/science.284.5423.2124

J. P. Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szöllösi, V. Ranwez et al., An Efficient Algorithm for Gene/Species Trees Parsimonious Reconciliation with Losses, Duplications and Transfers, Proceedings of the Eighth RECOMB Comparative Genomics Satellite Workshop (RECOMB-CG'10), pp.93-108, 2011.
DOI : 10.1007/978-3-642-16181-0_9

URL : https://hal.archives-ouvertes.fr/lirmm-00818889

P. Gambette, V. Berry, and C. Paul, The Structure of Level-k Phylogenetic Networks, pp.289-300, 2009.
DOI : 10.1089/cmb.2005.12.796

URL : https://hal.archives-ouvertes.fr/lirmm-00371485

M. R. Garey and D. S. Johnson, Complexity Results for Multiprocessor Scheduling under Resource Constraints, SIAM Journal on Computing, vol.4, issue.4, pp.397-411, 1975.
DOI : 10.1137/0204035

M. R. Garey and D. S. Johnson, A guide to the theory of NP-completeness, Series of Books in the Mathematical Sciences, 1979.

J. Gramm, A. Nickelsen, and T. Tantau, Fixed-Parameter Algorithms in Phylogenetics, The Computer Journal, vol.51, issue.1, pp.79-101, 2008.
DOI : 10.1093/comjnl/bxm049

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

J. C. Hotopp, Horizontal gene transfer between bacteria and animals, Trends in Genetics, vol.27, issue.4, pp.157-163, 2011.
DOI : 10.1016/j.tig.2011.01.005

K. T. Huber, L. Van-iersel, V. Moulton, and T. Wu, How Much Information is Needed to Infer Reticulate Evolutionary Histories?, Systematic Biology, vol.64, issue.1, pp.102-111, 2015.
DOI : 10.1093/sysbio/syu076

D. H. Huson, R. Rupp, and C. Scornavacca, Phylogenetic networks: concepts, algorithms and applications, 2010.
DOI : 10.1017/CBO9780511974076

D. H. Huson and C. Scornavacca, A Survey of Combinatorial Methods for Phylogenetic Networks, Genome Biology and Evolution, vol.3, issue.0, pp.23-35, 2011.
DOI : 10.1093/gbe/evq077

L. Van-iersel, Algorithms, haplotypes and phylogenetic networks, 2009.

L. Van-iersel and V. Moulton, Trinets encode tree-child and level-2 phylogenetic networks, Journal of Mathematical Biology, vol.8, issue.3, pp.1707-1729, 2014.
DOI : 10.1007/s00285-013-0683-5

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

J. Jansson and W. K. Sung, Inferring a level-1 phylogenetic network from a dense set of rooted triplets, Theoretical Computer Science, vol.363, issue.1, pp.60-68, 2006.
DOI : 10.1016/j.tcs.2006.06.022

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

L. S. Kubatko, Identifying Hybridization Events in the Presence of Coalescence via Model Selection, Systematic Biology, vol.58, issue.5, pp.478-488, 2009.
DOI : 10.1093/sysbio/syp055

J. Mallet, Hybrid speciation, Nature, vol.77, issue.7133, pp.279-283, 2007.
DOI : 10.1038/nature05706

C. Meng and L. S. Kubatko, Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model, Theoretical Population Biology, vol.75, issue.1, pp.35-45, 2009.
DOI : 10.1016/j.tpb.2008.10.004

D. A. Morrison, Introduction to Phylogenetic Networks, 2011.

A. W. 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

F. Pardi and C. Scornavacca, Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable, PLOS Computational Biology, vol.7, issue.4, p.135, 2015.
DOI : 10.1371/journal.pcbi.1004135.s001

URL : https://hal.archives-ouvertes.fr/lirmm-01237428

D. Posada, K. A. Crandall, and E. C. Holmes, Recombination in Evolutionary Genomics, Annual Review of Genetics, vol.36, issue.1, pp.75-97, 2002.
DOI : 10.1146/annurev.genet.36.040202.111115

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

S. Vuilleumier and S. Bonhoeffer, Contribution of recombination to the evolutionary history of HIV, Current Opinion in HIV and AIDS, vol.10, issue.2, pp.84-89, 2015.
DOI : 10.1097/COH.0000000000000137

T. J. Warnow, Tree Compatibility and Inferring Evolutionary History, Journal of Algorithms, vol.16, issue.3, pp.388-407, 1994.
DOI : 10.1006/jagm.1994.1018

Y. Yu, J. H. 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

Y. Yu, J. Dong, K. J. Liu, and L. Nakhleh, Maximum likelihood inference of reticulate evolutionary histories, Proceedings of the National Academy of Sciences, vol.111, issue.46, pp.448-16453, 2014.
DOI : 10.1073/pnas.1407950111

O. Zhaxybayeva and W. F. Doolittle, Lateral gene transfer, Current Biology, vol.21, issue.7, pp.242-246, 2011.
DOI : 10.1016/j.cub.2011.01.045