Computing galled networks from real data

Bioinformatics

Volumn 25, Issue 12, 2009, Pages

  Huson, Daniel H ^a   Rupp, Regula ^a   Berry, Vincent ^b   Gambette, Philippe ^b   Paul, Christophe ^b  

^a UNIVERSITY OF TÜBINGEN   (Germany)

^b CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOINFORMATICS; COMPUTER PROGRAM; CONFERENCE PAPER; DATA BASE; INFORMATION PROCESSING; MATHEMATICAL COMPUTING; MOLECULAR PHYLOGENY; NONHUMAN; PHYLOGENETIC TREE; PRIORITY JOURNAL; PROKARYOTE; STATISTICAL ANALYSIS; TAXON;

COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; NEURAL NETWORKS (COMPUTER); PHYLOGENY; SOFTWARE;

PROKARYOTA;

EID: 66349108852     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btp217     Document Type: Conference Paper

References (32)

1. Bandelt,H.J. and Dress,A.W.M. (1992) A canonical decomposition theory for metrics on a finite set. Adv. Math., 92, 47-105.
2. Berry,V. and Nicolas,F. (2006) Improved parameterized complexity of the maximum agreement subtree and maximum compatible tree problems. IEEE/ ACM TCBB, 3, 289-302.
3. Bordewich,M. et al. (2007) A reduction algorithm for computing the hybridization number of two trees. Evol. Bioinform., 3, 86-98.
4. Bryant,D. and Moulton,V. (2002) NeighborNet: An agglomerative method for the construction of planar phylogenetic networks. In Guigó,R. and Gusfield,D. (eds), Algorithms in Bioinformatics, WABI 2002. vol. 2452, Lecture Notes in Computer Science, Springer Berlin/ Heidelberg, pp. 375-391.
5. Charbit,P. et al. (2008) A note on computing set overlap classes. Inform. Process. Lett., 108, 186-191.
6. Cohen,J.E. (2004) Mathematics is Biology's next microscope, only better; Biology is Mathematics' next Physics, only better. PLoS Biol., 2, e439.
7. Doolittle,W.F. and Bapteste,E. (2007) Pattern pluralism and the tree of life hypothesis. Proc. Natl Acad. Sci. USA, 104, 2043-2049.
8. Grass Phylogeny Working Group. (2001) Phylogeny and subfamilial classification of the grasses (poaceae). Ann. M. Bot. Gard., 88 373-457.
9. Gusfield,D. and Bansal,V. (2005) A fundamental decomposition theory for phylogenetic networks and incompatible characters. In Proceedings of the Ninth International Conference on Research in Computational Molecular Biology (RECOMB). Cambridge, MA, USA, pp. 217-232.
10. Gusfield,D. et al. (2003) Efficient reconstruction of phylogenetic networks with constrained recombination. In Proceedings of the IEEE Computer Society Conference on Bioinformatics. Stanford, CA, USA, pp. 363.
11. Gusfield,D. et al. (2007) A decomposition theory for phylogenetic networks and incompatible characters. J. Computat. Biol., 14 1247-1272.
12. Hallett,M. and Lagergren,J. (2001) Efficient algorithms for lateral gene transfer problems. In 5th Annual RECOMB Montreal, April 22-25, pp. 149-156.
13. Hein,J. (1993) A heuristic method to reconstruct the history of sequences subject to recombination. J. Mol. Evol. 36, 396-405.
14. Huber,K.T.et al.(2007) Reconstructing the evolutionary history of polyploids from multilabeled trees. Mol. Biol. Evol., 23, 1784-1791.
15. Huson,D.H. and Kloepper,T.H. (2005) Computing recombination networks from binary sequences. Bioinformatics, 21 (Suppl. 2), ii159-ii165. ECCB.
16. Huson,D.H. and Bryant,D. (2006) Application of phylogenetic networks in evolutionary studies. Mol. Biol. Evol., 23, 254-267.
17. Huson,D.H and Kloepper,T.H. (2007) Beyond galled trees - decomposition and computation of galled networks. In Proceedings of the Eleventh International Conference on Research in Computational Molecular Biology (RECOMB). Vol. 4453 of Lecture Notes in Computer Science, Oakland, CA, USA, pp. 211-225.
18. Huson,D.H. and Rupp,R. (2008) Summarizing multiple gene trees using cluster networks. In Crandall,K. and Lagergren,J. (eds), Algorithms in Bioinformatics, WABI 2008. Vol. 5251 in Lecture Notes in Bioinformatics (LNBI). Springer, Berlin/Heidelberg, pp. 211-225.
19. Huson,D.H. et al. (2004) Phylogenetic super-networks from partial trees. IEEE/ACM TCBB, 1, 151-158.
20. Huson,D.H. et al. (2005) Reconstruction of reticulate networks from gene trees. In Proceedings of the Ninth International Conference on Research in Computational Molecular Biology (RECOMB), Vol. 3500 of Lecture Notes in Computer Science. Springer Verlag, Heidelberg, pp. 233-249.
21. Huson,D.H. et al. (2007) Dendroscope: An interactive viewer for large phylogenetic trees. BMC Bioinformatics, 8, 460.
22. Kanj,I.A. et al. (2008) Seeing the trees and their branches in the network is hard. Theor. Comput. Sci., 401, 153-164.
23. Linder,C.R. and Rieseberg,L.H. (2004) Reconstructing patterns of reticulate evolution in plants. Am. J. Bot., 91, 1700-1708.
24. Lyngsø,R.B. et al. (2005) Minimum recombination histories by branch and bound. In Proceedings of the Workshop on Algorithms in Bioinformatics (WABI). Mallorca, Spain, pp. 239-250.
25. Ma,B.et al. (1998) Fixed topology alignment with recombination. In Proceedings of the 9th Annual Symposium on Combinatorial Pattern Matching (CPM'98). Vol. 1448 of Lecture Notes in Computer Science pp. 174-188.
26. Mirkin,B.G. et al. (2003) Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and domiance of horizontal gene transfer in the evolution of prokaryotes. BMC Evol. Biol., 3, 2.
27. Steel,M. and Hamel,A. (1996) Finding a maximum compatible tree is NP-hard for sequences and trees. Appl. Math. Lett., 9, 55-60.
28. Song,Y.S. and Hein,J. (2005) Constructing minimal ancestral recombination graphs. J. Comp. Biol., 12, 147-169.
29. Than,C. et al. (2008) Phylonet: A software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics, 9, 1-16.
30. van Iersel,L. and Kelk,S. (2008) Constructing the simplest possible phylogenetic network from triplets. In Proceedings of ISAAC'08, Vol. 5369, Springer, Berlin/Heidelberg, Gold Coast, Australia, pp. 472-483.
31. van Iersel,L. et al. (2008) Constructing level-2 phylogenetic networks from triplets. In International Conference on Computational Molecular Biology (RECOMB). Vol. 4955 of Lecture Notes in Computer Science, Springer Verlag, Berlin/Heidelberg, pp. 450-462.
32. Wang,L. et al. (2001) Perfect phylogenetic networks with recombination. In Proceedings of the 16th ACM Symposium on Applied Computing (SAC'01). Las Vegas, NV, USA, pp. 46-50.