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BioMed Research International
Volume 2013 (2013), Article ID 472163, 10 pages
http://dx.doi.org/10.1155/2013/472163
Research Article

Algorithms of Ancestral Gene Length Reconstruction

1Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, 199 Aba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel
2Institute of Evolution, University of Haifa, Mount Carmel., Haifa 39105, Israel
3The Tauber Bioinformatics Center, University of Haifa, 199 Aba-Hushi Avenue, Mount Carmel, Haifa 3498838, Israel

Received 30 August 2013; Accepted 24 September 2013

Academic Editor: Vassily Lyubetsky

Copyright © 2013 Alexander Bolshoy and Valery M. Kirzhner. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. D. A. Liberles, Ed., Ancestral Sequence Reconstruction, Oxford University Press, Oxford, UK, 2007.
  2. W. M. Fitch, “Towards defining the course of evolution: minimum change for a specific tree topology,” Systematic Zoology, vol. 20, pp. 406–416, 1971.
  3. D. Sankoff and P. Rousseau, “Locating the vertices of a steiner tree in an arbitrary metric space,” Mathematical Programming, vol. 9, no. 1, pp. 240–246, 1975. View at Publisher · View at Google Scholar · View at Scopus
  4. D. Sankoff, “Minimal mutation trees of sequences,” SIAM Journal on Applied Mathematics, vol. 28, no. 1, pp. 35–42, 1975. View at Scopus
  5. T. Pupko, A. Doron-Faigenboim, D. A. Liberles, and G. M. Cannarozzi, “Probabilistic models and their impact on the accuracy of reconstructed ancestral protein sequences,” in Ancestral Sequence Reconsruction, D. A. Liberles, Ed., Oxford Oxford University Press, 2007.
  6. H. Ashkenazy, O. Penn, A. Doron-Faigenboim et al., “FastML: a web server for probabilistic reconstruction of ancestral sequences,” Nucleic Acids Research, vol. 40, pp. W580–W584, 2012.
  7. A. Bolshoy and Z. Volkovich, “Whole-genome prokaryotic clustering based on gene lengths,” Discrete Applied Mathematics, vol. 157, no. 10, pp. 2370–2377, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. F. R. K. Chung, “Some problems and results in labelings of graphs,” in The Theory and Applications of Graphs, G. Chartland, Ed., pp. 255–263, John Wiley & Sons, New York, NY, USA, 1981.
  9. M. A. Iordanskii, “Minimal numberings of the vertices of trees,” Soviet Mathematics Doklady, vol. 15, pp. 1311–1315, 1974.
  10. M. K. Goldberg and I. Klipker, “An algorithm for a minimal placement of a tree on a line,” Sakartvelos Mecnierebata Akademiis Moambe, vol. 83, pp. 553–556, 1976 (Russian).
  11. F. R. K. Chung, “On optimal linear arrangements of trees,” Computers and Mathematics with Applications, vol. 10, no. 1, pp. 43–60, 1984. View at Scopus
  12. F. R. K. Chung, “On the cutwidth and the topological bandwidth of a tree,” SIAM Journal on Algebraic and Discrete Methods, vol. 6, pp. 268–277, 1985.
  13. A. Bolshoy and V. Kirzhner, “Algorithms of an optimal integer tree labeling,” http://arxiv.org/abs/1305.5551.
  14. B. G. Mirkin, T. I. Fenner, M. Y. Galperin, and E. V. Koonin, “Algorithms for computing parsimonious evolutionary scenarios for genome evolution, the last universal common ancestor and dominance of horizontal gene transfer in the evolution of prokaryotes,” BMC Evolutionary Biology, vol. 3, no. 1, article 2, 2003. View at Scopus
  15. J. S. Farris, “Methods for computing Wagner trees,” Systematic Zoology, vol. 19, pp. 83–92, 1970.
  16. K. Y. Gorbunov and V. A. Lyubetsky, “Reconstructing the evolution of genes along the species tree,” Molecular Biology, vol. 43, no. 5, pp. 881–893, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. K. Y. Gorbunov and V. A. Lyubetsky, “An algorithm of reconciliation of gene and species trees and inferring gene duplications, losses and horizontal transfers,” Information Processes, vol. 10, pp. 140–144, 2010 (Russian).
  18. J.-P Doyon, C. Scornavacca, K. Y. Gorbunov, G. J. Szeollosi, V. Ranwez, and V. Berry, “An efficient algorithm for gene/species trees parsimonious reconciliation with losses, duplications and transfers,” in Lecture Notes in Bioinformatics, S. Istrail, P. Pevzner, and M. Waterman, Eds., vol. 6398 of Subseries of Lecture Notes in Computer Science, pp. 93–108, Springer, Berlin, Germany, 2010.
  19. K. Y. Gorbunov and V. A. Lyubetsky, “The tree nearest on average to a given set of trees,” Problems of Information Transmission, vol. 47, no. 3, pp. 274–288, 2011. View at Publisher · View at Google Scholar · View at Scopus
  20. K. Y. Gorbunov and V. A. Lyubetsky, “Fast algorithm to reconstruct a species supertree from a set of protein trees,” Molecular Biology, vol. 46, no. 1, pp. 161–167, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. V. A. Lyubetsky, L. I. Rubanov, L. Y. Rusin, and K. Y. Gorbunov, “Cubic time algorithms of amalgamating gene trees and building evolutionary scenarios,” Biology Direct, vol. 7, pp. 1–20, 2012.
  22. L. Y. Rusin, E. V. Lyubetskaya, K. Y. Gorbunov, and V. A. Lyubetsky, “Reconciliation of gene and species trees,” BioMed Research International. In press.