
This Article  
 
Share  
Bibliographic References  
Add to:  
Digg Furl Spurl Blink Simpy Del.icio.us Y!MyWeb  
Search  
 
ASCII Text  x  
Leo van Iersel, Judith Keijsper, Steven Kelk, Leen Stougie, Ferry Hagen, Teun Boekhout, "Constructing Level2 Phylogenetic Networks from Triplets," IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 4, pp. 667681, OctoberDecember, 2009.  
BibTex  x  
@article{ 10.1109/TCBB.2009.22, author = {Leo van Iersel and Judith Keijsper and Steven Kelk and Leen Stougie and Ferry Hagen and Teun Boekhout}, title = {Constructing Level2 Phylogenetic Networks from Triplets}, journal ={IEEE/ACM Transactions on Computational Biology and Bioinformatics}, volume = {6}, number = {4}, issn = {15455963}, year = {2009}, pages = {667681}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2009.22}, publisher = {IEEE Computer Society}, address = {Los Alamitos, CA, USA}, }  
RefWorks Procite/RefMan/Endnote  x  
TY  JOUR JO  IEEE/ACM Transactions on Computational Biology and Bioinformatics TI  Constructing Level2 Phylogenetic Networks from Triplets IS  4 SN  15455963 SP667 EP681 EPD  667681 A1  Leo van Iersel, A1  Judith Keijsper, A1  Steven Kelk, A1  Leen Stougie, A1  Ferry Hagen, A1  Teun Boekhout, PY  2009 KW  Phylogenetic networks KW  level2 KW  triplets KW  reticulations KW  polynomial time algorithms. VL  6 JA  IEEE/ACM Transactions on Computational Biology and Bioinformatics ER   
[1] A.V. Aho, Y. Sagiv, T.G. Szymanski, and J.D. Ullman, “Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions,” SIAM J. Computing, vol. 10, no. 3, pp. 405421, 1981.
[2] D. Bryant, “Building Trees, Hunting for Trees, and Comparing Trees: Theory and Methods in Phylogenetic Analysis,” PhD dissertation, Univ. of Canterbury, 1997.
[3] D. Bryant and V. Moulton, “NeighborNet: An Agglomerative Method for the Construction of Phylogenetic Networks,” Molecular Biology and Evolution, vol. 21, no. 2, pp. 255265, 2004.
[4] D. Bryant and M. Steel, “Constructing Optimal Trees from Quartets,” J. Algorithms, vol. 38, no. 1, pp. 237259, 2001.
[5] J. Byrka, P. Gawrychowski, K.T. Huber, and S. Kelk, “WorstCase Optimal Approximation Algorithms for Maximizing Triplet Consistency within Phylogenetic Networks,” arXiv:0710.3258v3 [qbio.PE], 2008.
[6] H.L. Chan, J. Jansson, T.W. Lam, and S.M. Yiu, “Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix,” J. Bioinformatics and Computational Biology, vol. 4, no. 4, pp. 807832, 2006.
[7] P.L. Erdös, M.A. Steel, L.A. Szekely, and T. Warnow, “A Few Logs Suffice to Build (Almost) All Trees (Part II),” Theoretical Computer Science, vol. 221, no. 1, pp. 77118, 1999.
[8] L. Gaasieniec, J. Jansson, A. Lingas, and A. Östlin, “On the Complexity of Constructing Evolutionary Trees,” J. Combinatorial Optimization, vol. 3, pp. 183197, 1999.
[9] S. Guindon and O. Gascuel, “A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood,” Systematic Biology, vol. 52, no. 5, pp. 696704, 2003.
[10] D. Gusfield, S. Eddhu, and C. Langley, “Optimal, Efficient Reconstruction of Phylogenetic Networks with Constrained Recombination,” J. Bioinformatics and Computational Biology, vol. 2, pp. 173213, 2004.
[11] Y.J. He, T.N.D. Huynh, J. Jansson, and W.K. Sung, “Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets,” J. Bioinformatics and Computational Biology, vol. 4, no. 1, pp. 5974, 2006.
[12] M. Holder and P.O. Lewis, “Phylogeny Estimation: Traditional and Bayesian Approaches,” Nature Rev. Genetics, vol. 4, pp. 275284, 2003.
[13] K.T. Huber, B. Oxelman, M. Lott, and V. Moulton, “Reconstructing the Evolutionary History of Polyploids from Multilabeled Trees,” Molecular Biology and Evolution, vol. 23, no. 9, pp. 17841791, 2006.
[14] D.H. Huson and D. Bryant, “Application of Phylogenetic Networks in Evolutionary Studies,” Molecular Biology and Evolution, vol. 23, no. 2, pp. 254267, 2006.
[15] D.H. Huson and T.H. Klöpper, “Beyond Galled Trees—Decomposition and Computation of Galled Networks,” Proc. Int'l Conf. Research in Computational Molecular Biology (RECOMB '07), pp.211225, 2007.
[16] L.J.J. van Iersel, J.C.M. Keijsper, S.M. Kelk, and L. Stougie, “Constructing Level2 Phylogenetic Networks from Triplets,” arXiv:0707.2890v1 [qbio.PE], 2007.
[17] L.J.J. van Iersel, J.C.M. Keijsper, S.M. Kelk, L. Stougie, F. Hagen, and T. Boekhout, “Constructing Level2 Phylogenetic Networks from Triplets,” Proc. 12th Ann. Int'l Conf. Research in Computational Molecular Biology (RECOMB '08), pp. 450462, 2008.
[18] L.J.J. van Iersel, S.M. Kelk, and M. Mnich, “Uniqueness, Intractability and Exact Algorithms: Reflections on Levelk Phylogenetic Networks,” to be published in J. Bioinformatics and Computational Biology.
[19] J. Jansson, personal communication, Kyushu Univ., 2007.
[20] J. Jansson, “On the Complexity of Inferring Rooted Evolutionary Trees,” Proc. Brazilian Symp. Graphs, Algorithms and Combinatorics (GRACO '01), pp. 121125, 2001.
[21] J. Jansson, J.H.K. Ng, K. Sadakane, and W.K. Sung, “Rooted Maximum Agreement Supertrees,” Algorithmica, vol. 43, pp. 293307, 2005.
[22] J. Jansson, N.B. Nguyen, and W.K. Sung, “Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network,” SIAM J. Computing, vol. 35, no. 5, pp. 10981121, 2006.
[23] J. Jansson and W.K. Sung, “Inferring a Level1 Phylogenetic Network from a Dense Set of Rooted Triplets,” Proc. Conf. Computing and Combinatorics (COCOON '04), pp. 462472, 2004.
[24] J. Jansson and W.K. Sung, “Inferring a Level1 Phylogenetic Network from a Dense Set of Rooted Triplets,” Theoretical Computer Science, vol. 363, pp. 6068, 2006.
[25] T. Jiang, P.E. Kearney, and M. Li, “A Polynomial Time Approximation Scheme for Inferring Evolutionary Trees from Quartet Topologies and Its Application,” SIAM J. Computing, vol. 30, no. 6, pp. 19421961, 2000.
[26] S. Kidd, F. Hagen, R. Tscharke, M. Huynh, K. Bartlett, M. Fyfe, L. MacDougall, T. Boekhout, K.J. KwonChung, and W. Meyer, “A Rare Genotype of Cryptococcus Gattii Caused the Cryptococcosis Outbreak on Vancouver Island (British Columbia, Canada),” Proc. Nat'l Academy of Sciences USA, vol. 101, pp.1725817263, 2004.
[27] “LEVEL2: A Fast Method for Constructing Level2 Phylogenetic Networks from Dense Sets of Rooted Triplets,” http://home pages.cwi.nl/~kelklevel2triplets.html and http:/level2.source forge.net/, 2009.
[28] V. Makarenkov, “TREX: Reconstructing and Visualizing Phylogenetic Trees and Reticulation Networks,” Bioinformatics, vol. 17, no. 7, pp. 664668, 2001.
[29] V. Makarenkov, D. Kevorkov, and P. Legendre, “Phylogenetic Network Reconstruction Approaches,” Applied Mycology and Biotechnology, vol. 6. pp. 6197, 2006.
[30] B.M.E. Moret, L. Nakhleh, T. Warnow, C.R. Linder, A. Tholse, A. Padolina, J. Sun, and R. Timme, “Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy,” IEEE/ACM Trans. Computational Biology and Bioinformatics, vol. 1, no. 1, pp. 1323, Jan.Mar. 2004.
[31] C. Semple and M. Steel, Phylogenetics. Oxford Univ. Press, 2003.
[32] M. Steel, “The Complexity of Reconstructing Trees from Qualitative Characters and Subtrees,” J. Classification, vol. 9, pp. 91116, 1992.
[33] R.E. Tarjan and U. Vishkin, “An Efficient Parallel Biconnectivity Algorithm,” SIAM J. Computing, vol. 14, no. 4, pp. 862874, 1985.
[34] L. Wang, K. Zhang, and L. Zhang, “Perfect Phylogenetic Networks with Recombination,” J. Computational Biology, vol. 8, no. 1, pp. 6978, 2001.
[35] B.Y. Wu, “Constructing the Maximum Consensus Tree from Rooted Triples,” J. Combinatorial Optimization, vol. 8, pp. 2939, 2004.