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Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks

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WALCOM: Algorithms and Computation (WALCOM 2020)

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Abstract

Galled trees are studied as a recombination model in theoretical population genetics. Tree-child networks, reticulation-visible networks and tree-based networks can be considered as the generalizations of galled trees through relaxing a structural condition. Although these networks are simple, their topological structures have yet to be fully understood. Here, recent progresses in the tree and cluster containment problems and network counting problems are summarized.

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References

  1. Cardona, G., Rossello, F., Valiente, G.: Comparison of tree-child phylogenetic networks. IEEE/ACM Trans. Comput. Biol. Bioinform. 6(4), 552–569 (2009)

    Article  Google Scholar 

  2. Doolittle, W.F.: Phylogenetic classification and the universal tree. Science 284, 2124–2128 (1999)

    Article  Google Scholar 

  3. Francis, A., Steel, M.: Which phylogenetic networks are merely trees with additional arcs? Syst. Biol. 64(5), 768–777 (2015)

    Article  Google Scholar 

  4. Gambette, P., Gunawan, A.D., Labarre, A., Vialette, S., Zhang, L.: Solving the tree containment problem in linear time for nearly stable phylogenetic networks. Discret. Appl. Math. 246, 62–79 (2018)

    Article  MathSciNet  Google Scholar 

  5. Gunawan, A.D.M.: Solving the tree containment problem for reticulation-visible networks in linear time. In: Jansson, J., Martín-Vide, C., Vega-Rodríguez, M.A. (eds.) AlCoB 2018. LNCS, vol. 10849, pp. 24–36. Springer, Cham (2018). https://doi.org/10.1007/978-3-319-91938-6_3

    Chapter  Google Scholar 

  6. Gunawan, A.D., DasGupta, B., Zhang, L.: A decomposition theorem and two algorithms for reticulation-visible networks. Inform. Comput. 252, 161–175 (2017)

    Article  MathSciNet  Google Scholar 

  7. Gunawan, A.D., Lu, B., Zhang, L.: A program for verification of phylogenetic network models. Bioinformatics 32, i503–i510 (2016)

    Article  Google Scholar 

  8. Gunawan, A.D., Yan, H., Zhang, L.: Compression of phylogenetic networks and algorithm for the tree containment problem. J. Comput. Biol. 26, 285–294 (2019)

    Article  MathSciNet  Google Scholar 

  9. Gusfield, D.: ReCombinatorics: The Algorithmics of Ancestral Recombination Graphs and Explicit Phylogenetic Networks. MIT Press, Boston (2014)

    Book  Google Scholar 

  10. Gusfield, D., Eddhu, S., Langley, C.: The fine structure of galls in phylogenetic networks. INFORMS J. Comput. 16(4), 459–469 (2004)

    Article  MathSciNet  Google Scholar 

  11. Huson, D.H., Klöpper, T.H.: Beyond galled trees - decomposition and computation of galled networks. In: Speed, T., Huang, H. (eds.) RECOMB 2007. LNCS, vol. 4453, pp. 211–225. Springer, Heidelberg (2007). https://doi.org/10.1007/978-3-540-71681-5_15

    Chapter  Google Scholar 

  12. Huson, D.H., Rupp, R., Scornavacca, C.: Phylogenetic Networks: Concepts Algorithms and Applications. Cambridge University Press, Cambridge (2010)

    Book  Google Scholar 

  13. Steel, M.: Phylogeny: Discrete and Random Processes in Evolution. SIAM, Philadelphia (2016)

    Book  Google Scholar 

  14. Wang, L., Zhang, K., Zhang, L.: Perfect phylogenetic networks with recombination. J. Comput. Biol. 8(1), 69–78 (2001)

    Article  Google Scholar 

  15. Weller, M.: Linear-time tree containment in phylogenetic networks. In: Blanchette, M., Ouangraoua, A. (eds.) RECOMB-CG 2018. LNCS, vol. 11183, pp. 309–323. Springer, Cham (2018). https://doi.org/10.1007/978-3-030-00834-5_18

    Chapter  Google Scholar 

  16. Willson, S.J.: Unique determination of some homoplasies at hybridization events. Bull. Math. Biol. 69, 1709–1725 (2007)

    Article  MathSciNet  Google Scholar 

  17. Yan, H., Gunawan, A.D., Zhang, L.: S-cluster++: a fast program for solving the cluster containment problem for phylogenetic networks. Bioinformatics 34(17), i680–i686 (2018)

    Article  Google Scholar 

  18. Zhang, L.: On tree-based phylogenetic networks. J. Comput. Biol. 23(7), 553–565 (2016)

    Article  MathSciNet  Google Scholar 

  19. Zhang, L.: Clusters, trees, and phylogenetic network classes. In: Warnow, T. (ed.) Bioinformatics and Phylogenetics. CB, vol. 29, pp. 277–315. Springer, Cham (2019). https://doi.org/10.1007/978-3-030-10837-3_12

    Chapter  Google Scholar 

  20. Zhang, L.: Generating normal networks via leaf insertion and nearest neighbor interchange. BMC Bioinform. 20, article no. 642 (2019)

    Google Scholar 

  21. Zhang, L.: Counting tree-child networks and their subclasses. arXiv preprint arXiv:1908.01917 (2019)

Download references

Acknowledgments

The author thanks B. DasGupta, P. Gambette, A. Gunawan, A. Labarre, S. Vialette, BX Liu and HW Yan for their collaboration in studying the combinatorial and algorithmic aspects of phylogenetic networks. This work was supported by Singapore-France Institute Merlion project and Singapore’s Ministry of Education Academic Research Fund Tier-1 [grant R-146-000-238-114].

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Authors and Affiliations

  1. Department of Mathematics, National University of Singapore, Singapore, 119076, Singapore

    Louxin Zhang

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  1. Louxin Zhang
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Correspondence to Louxin Zhang .

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Editors and Affiliations

  1. Department of CSE, BUET, Dhaka, Bangladesh

    M. Sohel Rahman

  2. Mathematical Informatics, University of Tokyo, Tokyo, Japan

    Kunihiko Sadakane

  3. School of Computing, National University of Singapore, Singapore, Singapore

    Wing-Kin Sung

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Zhang, L. (2020). Recent Progresses in the Combinatorial and Algorithmic Study of Rooted Phylogenetic Networks. In: Rahman, M., Sadakane, K., Sung, WK. (eds) WALCOM: Algorithms and Computation. WALCOM 2020. Lecture Notes in Computer Science(), vol 12049. Springer, Cham. https://doi.org/10.1007/978-3-030-39881-1_3

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  • DOI: https://doi.org/10.1007/978-3-030-39881-1_3

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  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-030-39880-4

  • Online ISBN: 978-3-030-39881-1

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