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BioMed Research International
Volume 2013 (2013), Article ID 503193, 7 pages
http://dx.doi.org/10.1155/2013/503193
Research Article

Inferring Phylogenetic Networks from Gene Order Data

Limnological Institute of the Siberian Branch of the Russian Academy of Sciences, 3 Ulan-Batorskaya Street, Irkutsk 664033, Russia

Received 19 March 2013; Revised 4 July 2013; Accepted 20 July 2013

Academic Editor: Vassily Lyubetsky

Copyright © 2013 Alexey Anatolievich Morozov et al. 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. G. Fertin, A. Labarre, I. Rusu, E. Tannier, and S. Vialette, Combinatorics of Genome Rearrangements, The MIT Press, Boston, Mass, USA, 2009.
  2. D. D. Huson, R. Rupp, and C. Scornavacca, Phylogenetic Networks: Concepts, Algorithms and Applications, Cambridge University Press, Cambridge, UK, 2011.
  3. H. J. Bandelt and A. W. M. Dress, “A canonical decomposition theory for metrics on a finite set,” Advances in Mathematics, vol. 92, no. 1, pp. 47–105, 1992. View at Google Scholar · View at Scopus
  4. D. H. Huson and D. Bryant, “Application of phylogenetic networks in evolutionary studies,” Molecular Biology and Evolution, vol. 23, no. 2, pp. 254–267, 2006. View at Publisher · View at Google Scholar · View at Scopus
  5. S. Kang, J. Tang, S. W. Schaeffer, and D. A. Bader, “Rec-DCM-Eigen: reconstructing a less parsimonious but more accurate tree in shorter time,” PLoS ONE, vol. 6, no. 8, Article ID e22483, 2011. View at Publisher · View at Google Scholar · View at Scopus
  6. B. R. Holland, K. T. Huber, V. Moulton, and P. J. Lockhart, “Using consensus networks to visualize contradictory evidence for species phylogeny,” Molecular Biology and Evolution, vol. 21, no. 7, pp. 1459–1461, 2004. View at Publisher · View at Google Scholar · View at Scopus
  7. J. Tang and B. M. E. Moret, “Scaling up accurate phylogenetic reconstruction from gene-order data,” Bioinformatics, vol. 19, pp. 305–312, 2003. View at Google Scholar · View at Scopus
  8. D. Bryant and V. Moulton, “Neighbor-net: an agglomerative method for the construction of phylogenetic networks,” Molecular Biology and Evolution, vol. 21, no. 2, pp. 255–265, 2004. View at Publisher · View at Google Scholar · View at Scopus
  9. M. E. Cosner, R. K. Jansen, B. M. E. Moret et al., “An empirical comparison of phylogenetic methods on chloroplast gene order data in campanulaceae,” in Comparative Genomics: Empirical and Analytical Approaches to Gene Order Dynamics, Map Alignment and the Evolution of Gene Families, D. Sankoff and J. H. Nadeau, Eds., Kluwer Academic Publishers, Dordrecht, The Netherlands, 2000. View at Google Scholar
  10. H. J. Bandelt and A. Dress, “A relational approach to split decomposition,” in Information and Classification, O. Opitz, B. Lausen, and R. Klar, Eds., pp. 123–131, Springer, New York, NY, USA, 1993. View at Google Scholar
  11. G. Bourque and P. A. Pevzner, “Genome-scale evolution: reconstructing gene orders in the ancestral species,” Genome Research, vol. 12, no. 1, pp. 26–36, 2002. View at Google Scholar · View at Scopus
  12. B. Larget, J. B. Kadane, and D. L. Simon, “A Bayesian approach to the estimation of ancestral genome arrangements,” Molecular Phylogenetics and Evolution, vol. 36, no. 2, pp. 214–223, 2005. View at Publisher · View at Google Scholar · View at Scopus
  13. E. C. Theriot, M. Ashworth, E. Ruck, T. Nakov, and R. K. Jansen, “A preliminary multi gene phylogeny of the diatoms (Bacillariophyta): challenges for future research,” Plant Ecology and Evolution, vol. 143, no. 3, pp. 278–296, 2010. View at Publisher · View at Google Scholar · View at Scopus