Computing the rooted triplet distance between galled trees by counting triangles

Journal of Discrete Algorithms - Tập 25 - Trang 66-78 - 2014
Jesper Jansson1, Andrzej Lingas2
1Laboratory of Mathematical Bioinformatics, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan
2Department of Computer Science, Lund University, 22100 Lund, Sweden

Tài liệu tham khảo

Alon, 1997, Finding and counting given length cycles, Algorithmica, 17, 209, 10.1007/BF02523189 Bansal, 2011, Comparing and aggregating partially resolved trees, Theor. Comput. Sci., 412, 6634, 10.1016/j.tcs.2011.08.027 Brodal, 2013, Efficient algorithms for computing the triplet and quartet distance between trees of arbitrary degree, 1814 Cardona, 2009, Metrics for phylogenetic networks II: Nodal and triplets metrics, IEEE/ACM Trans. Comput. Biol. Bioinform., 6, 454, 10.1109/TCBB.2008.127 Cardona, 2011, Comparison of galled trees, IEEE/ACM Trans. Comput. Biol. Bioinform., 8, 410, 10.1109/TCBB.2010.60 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 Critchlow, 1996, The triples distance for rooted bifurcating phylogenetic trees, Syst. Biol., 45, 323, 10.1093/sysbio/45.3.323 Dobson, 1975, Comparing the shapes of trees, vol. 452, 95 Felsenstein, 2004 Gambette, 2012, On encodings of phylogenetic networks of bounded level, J. Math. Biol., 65, 157, 10.1007/s00285-011-0456-y Gusfield, 2004, Optimal, efficient reconstruction of phylogenetic networks with constrained recombination, J. Bioinform. Comput. Biol., 2, 173, 10.1142/S0219720004000521 Harel, 1984, Fast algorithms for finding nearest common ancestors, SIAM J. Comput., 13, 338, 10.1137/0213024 Huson, 2010 van Iersel, 2011, Constructing the simplest possible phylogenetic network from triplets, Algorithmica, 60, 207, 10.1007/s00453-009-9333-0 Jansson, 2006, Algorithms for combining rooted triplets into a galled phylogenetic network, SIAM J. Comput., 35, 1098, 10.1137/S0097539704446529 Kuhner, 1994, A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates, Mol. Biol. Evol., 11, 459 Morrison, 2011 Nakhleh, 2005, A comparison of phylogenetic reconstruction methods on an Indo-European dataset, Trans. Philol. Soc., 103, 171, 10.1111/j.1467-968X.2005.00149.x Nielsen, 2011, A sub-cubic time algorithm for computing the quartet distance between two general trees, Algorithms Mol. Biol., 6, 10.1186/1748-7188-6-15 Rosselló, 2009, All that glisters is not galled, Math. Biosci., 221, 54, 10.1016/j.mbs.2009.06.007 Semple, 2003, Phylogenetics, vol. 24 Wang, 2000, Fixed topology alignment with recombination, Discrete Appl. Math., 104, 281, 10.1016/S0166-218X(00)00196-7 Vassilevska, 2010, Finding heaviest H-subgraphs in real weighted graphs, with applications, ACM Trans. Algorithms, 6, 10.1145/1798596.1798597 Vassilevska Williams, 2012, Multiplying matrices faster than Coppersmith–Winograd, 887