D. Morrison, Networks in phylogenetic analysis: new tools for population biology, International Journal for Parasitology, vol.35, issue.5, pp.567-582, 2005.
DOI : 10.1016/j.ijpara.2005.02.007

P. Buneman, The recovery of trees from measures of dissimilarity, Mathematics in Archeological and Historical Sciences, pp.387-395, 1971.

V. Makarenkov and .. , T-REX: reconstructing and visualizing phylogenetic trees and reticulation networks, Bioinformatics, vol.17, issue.7, pp.664-668, 2001.
DOI : 10.1093/bioinformatics/17.7.664

J. Whitfield, . Sa-cameron, M. Huson, and . Steel, Filtered Z-Closure Supernetworks for Extracting and Visualizing Recurrent Signal from Incongruent Gene Trees, Systematic Biology, vol.57, issue.6, pp.939-947, 2008.
DOI : 10.1080/10635150802552849

. Br-holland, . Benthin, . Lockhart, K. Moulton, and . Huber, Using supernetworks to distinguish hybridization from lineage-sorting, BMC Evolutionary Biology, vol.8, issue.1, 2008.
DOI : 10.1186/1471-2148-8-202

A. Dress and D. Huson, Constructing splits graphs, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.1, issue.3, pp.109-115, 2004.
DOI : 10.1109/TCBB.2004.27

. Br-holland, V. Delsuc, and . Moulton, Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods, Systematic Biology, vol.54, issue.1, pp.66-76, 2005.
DOI : 10.1080/10635150590906055

S. Grünewald, A. Forslund, V. Dress, and . 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

S. Grünewald, . Spillner, V. Forslund, and . Moulton, Constructing Phylogenetic Supernetworks from Quartets, Proc 8 th Workshop Algorithms Bioinformatics (WABI'08), pp.284-295, 2008.
DOI : 10.1007/978-3-540-87361-7_24

D. Huson, . Kloepper, M. Lockhart, and . Steel, Reconstruction of Reticulate Networks from Gene Trees, Proc 9 th Annu Int Conf on Research in Computational Mol Biol (RECOMB'05), pp.233-249, 2005.
DOI : 10.1007/11415770_18

D. Huson and T. Kloepper, Beyond Galled Trees - Decomposition and Computation of Galled Networks, Proc 11 th Annu Int Conf on Research in, pp.211-225, 2007.
DOI : 10.1007/978-3-540-71681-5_15

T. Kloepper, Algorithms for the Calculation and Visualisation of Phylogenetic Networks, 2008.

O. Bininda-emonds, A. Beck, and . Purvis, Getting to the Roots of Matrix Representation, Systematic Biology, vol.54, issue.4, pp.668-672, 2005.
DOI : 10.1080/10635150590947113

J. Dufayard, . Duret, . Penel, . Gouy, G. Rechenmann et al., Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases, Bioinformatics, vol.21, issue.11, pp.2596-2603, 2005.
DOI : 10.1093/bioinformatics/bti325

URL : https://hal.archives-ouvertes.fr/hal-00427861

J. Huerta-cepas, S. Capella-gutierrez, L. Pryszcz, . Denisov, M. Kormes et al., PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions, Nucleic Acids Research, vol.39, issue.Database, pp.556-560, 2011.
DOI : 10.1093/nar/gkq1109

J. Jansson and W. 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

Y. He, . Huynh, W. Jansson, and . Sung, INFERRING PHYLOGENETIC RELATIONSHIPS AVOIDING FORBIDDEN ROOTED TRIPLETS, Journal of Bioinformatics and Computational Biology, vol.04, issue.01, pp.59-74, 2006.
DOI : 10.1142/S0219720006001709

J. Jansson, W. Nguyen, and . Sung, Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network, SIAM Journal on Computing, vol.35, issue.5, pp.1098-1121, 2006.
DOI : 10.1137/S0097539704446529

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

L. Van-iersel, . Keijsper, . Kelk, . Stougie, T. Hagen et al., Constructing Level-2 Phylogenetic Networks from Triplets, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, issue.4, pp.667-681, 2009.
DOI : 10.1109/TCBB.2009.22

L. Van, I. , and S. Kelk, Constructing the simplest possible phylogenetic network from triplets, Algorithmica, vol.60, issue.2, pp.207-235, 2011.

T. To and M. Habib, Level-k Phylogenetic Networks Are Constructable from a Dense Triplet Set in Polynomial Time, Proc 20 th Annu Symp Combinatorial Pattern Matching (CPM'09), pp.275-288, 2009.
DOI : 10.1007/978-3-540-78839-3_40

J. Byrka, . Gawrychowski, S. Huber, and . Kelk, Worst-case optimal approximation algorithms for maximizing triplet consistency within phylogenetic networks, Journal of Discrete Algorithms, vol.8, issue.1, pp.65-75, 2010.
DOI : 10.1016/j.jda.2009.01.004

URL : http://doi.org/10.1016/j.jda.2009.01.004

P. Gambette and K. Huber, On encodings of phylogenetic networks of bounded level, Journal of Mathematical Biology, vol.8, issue.3, 2012.
DOI : 10.1007/s00285-011-0456-y

URL : https://hal.archives-ouvertes.fr/hal-00609130

A. Aho, Y. Sagiv, J. Szymanski, and . Ullman, Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions, SIAM Journal on Computing, vol.10, issue.3, pp.405-421, 1981.
DOI : 10.1137/0210030

M. Steel, The complexity of reconstructing trees from qualitative characters and subtrees, Journal of Classification, vol.2, issue.2, pp.91-116, 1992.
DOI : 10.1007/BF02618470

D. Gusfield, . Bansal, Y. Bafna, and . Song, A Decomposition Theory for Phylogenetic Networks and Incompatible Characters, Journal of Computational Biology, vol.14, issue.10, pp.1247-1272, 2007.
DOI : 10.1089/cmb.2006.0137

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2581772

D. Gusfield, C. Eddhu, and . Langley, OPTIMAL, EFFICIENT RECONSTRUCTION OF PHYLOGENETIC NETWORKS WITH CONSTRAINED RECOMBINATION, Journal of Bioinformatics and Computational Biology, vol.02, issue.01, pp.173-213, 2004.
DOI : 10.1142/S0219720004000521

L. Van-iersel, M. Kelk, and . Mnich, UNIQUENESS, INTRACTABILITY AND EXACT ALGORITHMS: REFLECTIONS ON LEVEL-K PHYLOGENETIC NETWORKS, Journal of Bioinformatics and Computational Biology, vol.07, issue.04, pp.597-623, 2009.
DOI : 10.1142/S0219720009004308

S. Woolley, K. Posada, and . Crandall, A Comparison of Phylogenetic Network Methods Using Computer Simulation, PLoS ONE, vol.132, issue.4, p.1913, 2008.
DOI : 10.1371/journal.pone.0001913.s001

U. Brandes and S. Cornelsen, Phylogenetic graph models beyond trees, Discrete Applied Mathematics, vol.157, issue.10, pp.2361-2369, 2010.
DOI : 10.1016/j.dam.2008.06.031

URL : http://doi.org/10.1016/j.dam.2008.06.031

T. Tholey, Improved Algorithms for the 2-Vertex Disjoint Paths Problem, Proc 35 t h Int Conf Current Trends in Theory and Practice of Computer Science (SOFSEM'09), pp.546-557, 2009.
DOI : 10.1016/0020-0190(90)90071-5

S. Grünewald, V. Moulton, and A. Spillner, Consistency of the QNet algorithm for generating planar split networks from weighted quartets, Discrete Applied Mathematics, vol.157, issue.10, pp.2325-2334, 2009.
DOI : 10.1016/j.dam.2008.06.038

V. Berry and O. Gascuel, Inferring evolutionary trees with strong combinatorial evidence, Theoretical Computer Science, vol.240, issue.2, pp.271-298, 2000.
DOI : 10.1016/S0304-3975(99)00235-2

D. Harel and R. Tarjan, Fast Algorithms for Finding Nearest Common Ancestors, SIAM Journal on Computing, vol.13, issue.2, pp.338-355, 1984.
DOI : 10.1137/0213024

W. Guttmann and M. Maucher, Variations on an Ordering Theme with Constraints, Proc 4 th IFIP Int Conf on Theor Comp Sci (TCS'06), pp.77-90, 2006.
DOI : 10.1007/978-0-387-34735-6_10

P. Gambette, C. Berry, and . Paul, The Structure of Level-k Phylogenetic Networks, Proc 20 th Annu Symp Combinatorial Pattern Matching (CPM'09), pp.289-300, 2009.
DOI : 10.1089/cmb.2005.12.796

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

S. Kelk, C. Scornavacca, and L. Van-iersel, On the Elusiveness of Clusters, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.9, issue.2, 2012.
DOI : 10.1109/TCBB.2011.128