All that glisters is not galled

G. Cardona, F. Rosselló, G. Valiente, Comparison of tree-child phylogenetic networks, IEEE/ACM Trans. Comput. Biol. Bioinform. doi.ieeecomputersociety.org/10.1109/TCBB.2007.70270. Chan, 2006, Reconstructing an ultrametric galled phylogenetic network from a distance matrix, J. Bioinform. Comput. Biol., 4, 807, 10.1142/S0219720006002211 Choy, 2005, Computing the maximum agreement of phylogenetic networks, Theor. Comput. Sci., 335, 93, 10.1016/j.tcs.2004.12.012 Gusfield, 2005, Optimal efficient reconstruction of root-unknown phylogenetic networks with constrained and structured recombination, J. Comput. Syst. Sci., 70, 381, 10.1016/j.jcss.2004.12.009 Gusfield, 2007, A decomposition theory for phylogenetic networks and incompatible characters, J. Comput. Biol., 14, 1247, 10.1089/cmb.2006.0137 D. Gusfield, S. Eddhu, C. Langley, Efficient reconstruction of phylogenetic networks with constrained recombination, in: Proc. 2nd IEEE Computer Society Bioinformatics Conf., 2003. Gusfield, 2004, The fine structure of galls in phylogenetic networks, INFORMS J. Comput., 16, 459, 10.1287/ijoc.1040.0099 Gusfield, 2004, Optimal efficient reconstruction of phylogenetic networks with constrained recombination, J. Bioinform. Comput. Biol., 2, 173, 10.1142/S0219720004000521 Gusfield, 2007, An efficiently computed lower bound on the number of recombinations in phylogenetic networks: Theory and empirical study, Discrete Appl. Math., 155, 806, 10.1016/j.dam.2005.05.044 Hein, 1990, Reconstructing evolution of sequences subject to recombination using parsimony, Math. Biosci., 98, 185, 10.1016/0025-5564(90)90123-G D.H. Huson, T. Kloepper, Beyond galled trees – decomposition and computation of galled networks, in: Proc. 11th Annual Int. Conf. Research in Computational Molecular Biology, Lecture Notes in Computer Science, vol. 4453, Springer, 2007. Jansson, 2006, Algorithms for combining rooted triplets into a galled phylogenetic network, SIAM J. Comput., 35, 1098, 10.1137/S0097539704446529 J. Jansson, W.-K. Sung, The maximum agreement of two nested phylogenetic networks, in: Proc. 15th Int. Symp. Algorithms and Computation, Lecture Notes in Computer Science, vol. 3341, Springer, 2004. Jansson, 2006, Inferring a level-1 phylogenetic network from a dense set of rooted triplets, Theor. Comput. Sci., 363, 60, 10.1016/j.tcs.2006.06.022 Jansson, 2008, The maximum agreement of two nested phylogenetic networks, 119 Jin, 2006, Maximum likelihood of phylogenetic networks, Bioinformatics, 22, 2604, 10.1093/bioinformatics/btl452 Jin, 2007, Efficient parsimony-based methods for phylogenetic network reconstruction, Bioinformatics, 23, 123, 10.1093/bioinformatics/btl313 B. Ma, L. Wang, M. Li, Fixed topology alignment with recombination, in: Proc. 9th Annual Symp. Combinatorial Pattern Matching, Lecture Notes in Computer Science, vol. 1448, Springer, 1998. Nakhleh, 2005, Reconstructing reticulate evolution in species — theory and practice, J. Comput. Biol., 12, 796, 10.1089/cmb.2005.12.796 Semple, 2008, Hybridization networks, 277 Semple, 2006, Unicyclic networks: compatibility and enumeration, IEEE/ACM Trans. Comput. Biol. Bioinform., 2, 84, 10.1109/TCBB.2006.14 Song, 2005, Efficient computation of close lower and upper bounds on the minimum number of recombinations in biological sequence evolution, Bioinformatics, 21, i413, 10.1093/bioinformatics/bti1033 Strimmer, 2000, Likelihood analysis of phylogenetic networks using directed graphical models, Mol. Biol. Evol., 17, 875, 10.1093/oxfordjournals.molbev.a026367 L. van Iersel, J. Keijsper, S. Kelk, L. Stougie, F. Hagen, T. Boekhout, Constructing level-2 phylogenetic networks from triplets, in: Proc. 12th Annual Int. Conf. Research in Computational Molecular Biology, Lecture Notes in Bioinformatics, vol. 4955, Springer, 2008. L. van Iersel, S. Kelk, M. Mnich, Uniqueness, intractability and exact algorithms: reflections on level-k phylogenetic networks, J. Bioinform. Comput. Biol., in press. Wang, 2000, Fixed topology alignment with recombination, Discrete Appl. Math., 104, 281, 10.1016/S0166-218X(00)00196-7 Wang, 2001, Perfect phylogenetic networks with recombination, J. Comput. Biol., 8, 69, 10.1089/106652701300099119