Constructing level-2 phylogenetic networks from triplets

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 4955 LNBI, Issue , 2008, Pages 450-462

  Van Iersel, Leo ^a   Keijsper, Judith ^a   Kelk, Steven ^b   Stougie, Leen ^a,b   Hagen, Ferry ^c   Boekhout, Teun ^c  

^a EINDHOVEN UNIVERSITY OF TECHNOLOGY   (Netherlands)

^b CWI   (Netherlands)

^c CBS KNAW FUNGAL BIODIVERSITY CENTRE   (Netherlands)

Author keywords

[No Author keywords available]

Indexed keywords

BIOCHEMISTRY; HISTORY; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE; POLYNOMIAL APPROXIMATION; POLYNOMIALS;

COMPUTATIONAL MOLECULAR BIOLOGY; EVOLUTIONARY RELATIONSHIPS; HEIDELBERG (CO); INTERNATIONAL CONFERENCES; LEVEL-1; PHYLOGENETIC NETWORKS; POLYNOMIAL-TIME;

BIOLOGY;

EID: 47249122253     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-540-78839-3_40     Document Type: Conference Paper

References (26)

1. Aho, A.V., Sagiv, Y., Szymanski, T.G., Ullman, J.D.: Inferring a Tree from Lowest Common Ancestors with an Application to the Optimization of Relational Expressions. SIAM Journal on Computing 10(3), 405-421 (1981)
2. Bryant, D.: Building Trees, Hunting for Trees, and Comparing Trees: Theory and Methods in Phylogenetic Analysis, Ph.D. thesis, University of Canterbury, Christchurch, New Zealand (1997)
3. Bryant, D., Steel, M.: Constructing Optimal Trees from Quartets. Journal of Algorithms 38(1), 237-259 (2001)
4. Chan, H.-L., Jansson, J., Lam, T.W., Yiu, S.-M.: Reconstructing an Ultrametric Galled Phylogenetic Network from a Distance Matrix. Journal of Bioinformatics and Computational Biology 4(4), 807-832 (2006)
5. Erdös, P.L., Steel, M.A., Szekely, L.A., Warnow, T.: A few logs suffice to build (almost) all trees (Part II). Theoretical Computer Science 221(1), 77-118 (1999)
6. Ga̧sieniec, L., Jansson, J., Lingas, A., Östlin, A.: On the complexity of constructing evolutionary trees. Journal of Combinatorial Optimization 3, 183-197 (1999)
7. Guindon, S., Gascuel, O.: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology 52(5), 696-704 (2003)
8. Gusfield, D., Eddhu, S., Langley, C.: Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. Journal of Bioinformatics and Computational Biology 2, 173-213 (2004)
9. He, Y.-J., Huynh, T.N.D., Jansson, J., Sung, W.-K.: Inferring Phylogenetic Relationships Avoiding Forbidden Rooted Triplets. Journal of Bioinformatics and Computational Biology 4(1), 59-74 (2006)
10. Holder, M., Lewis, P.O.: Phylogeny estimation: Traditional and bayesian approaches. Nature Reviews Genetics 4, 275-284 (2003)
11. Huson, D.H., Bryant, D.: Application of Phylogenetic Networks in Evolutionary Studies. Molecular Biology and Evolution 23(2), 254-267 (2006)
12. Huson, D.H., Klöpper, T.H.: Beyond Galled Trees - Decomposition and Computation of Galled Networks. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS (LNBI), vol. 4453, pp. 211-225. Springer, Heidelberg (2007)
13. Iersel, L.J.J. van, Keijsper, J.C.M., Kelk, S.M., Stougie, L.: Constructing level-2 phylogenetic networks from triplets (preprint, 2007), http://arxiv.org/abs/0707.2890
14. Jansson, J.: On the complexity of inferring rooted evolutionary trees. In: proceedings of GRACO 2001, ENDM 7, pp. 121-125. Elsevier, Amsterdam (2001)
15. Jansson, J., Ng, J.H.-K., Sadakane, K., Sung, W.-K.: Rooted maximum agreement supertrees. Algorithmica 43, 293-307 (2005)
16. Jansson, J., Nguyen, N.B., Sung, W.-K.: Algorithms for Combining Rooted Triplets into a Galled Phylogenetic Network. SIAM Journal on Computing 35(5), 1098-1121 (2006)
17. Jansson, J., Sung, W.-K.: Inferring a Level-1 Phylogenetic Network from a Dense Set of Rooted Triplets. In: Chwa, K.-Y., Munro, J.I.J. (eds.) COCOON 2004. LNCS, vol. 3106, pp. 462-471. Springer, Heidelberg (2004)
18. Jansson, J., Sung, W.-K.: Inferring a Level-1 Phylogenetic Network from a Dense Set of Rooted Triplets. Theoretical Computer Science 363, 60-68 (2006)
19. Jiang, T., Kearney, P.E., Li, M.: A Polynomial Time Approximation Scheme for Inferring Evolutionary Trees from Quartet Topologies and Its Application. SIAM Journal on Computing 30(6), 1942-1961 (2000)
20. Kidd, S., Hagen, F., Tscharke, R., Huynh, M., Bartlett, K., Fyfe, M., MacDougall, L., Boekhout, T., Kwon-Chung, K.J., Meyer, W.: A rare genotype of Cryptococcus gattii caused the Cryptococcosis outbreak on Vancouver Island (British Columbia, Canada). In: Proceedings of the National Academy of Sciences of the United States of America, vol. 101, pp. 17258-17263 (2004)
21. LEVEL2: A fast method for constructing level-2 phylogenetic networks from dense sets of rooted triplets, http://homepages.cwi.nl/∼kelk/ level2triplets.html
22. Makarenkov, V., Kevorkov, D., Legendre, P.: Phylogenetic Network Reconstruction Approaches. In: Applied Mycology and Biotechnology. International Elsevier Series 6, Bioinformatics, vol. 6, pp. 61-97 (2006)
23. Moret, B.M.E., Nakhleh, L., Warnow, T., Linder, C.R., Tholse, A., Padolina, A., Sun, J., Timme, R.: Phylogenetic networks: modeling, reconstructibility, and accuracy. IEEE/ACM Transactions on Computational Biology and Bioinformatics 1(1), 13-23 (2004)
24. Semple, C., Steel, M.: Phylogenetics. Oxford University Press, Oxford (2003)
25. Steel, M.: The complexity of reconstructing trees from qualitative characters and subtrees. Journal of Classification 9, 91-116 (1992)
26. Wu, B.Y.: Constructing the maximum consensus tree from rooted triples. Journal of Combinatorial Optimization 8, 29-39 (2004)