Skip to main content

Two Results on Distances for Phylogenetic Networks

  • Conference paper

Part of the book series: Advances in Intelligent and Soft Computing ((AINSC,volume 74))

Abstract

We establish two new results on distances for phylogenetic networks. First, that Nakhleh’s metric for reduced networks [15] is a metric on the class of semibinary tree-sibling networks, being thus the only non-trivial metric computable in polynomial-time available so far on this class. And second, that a simple generalization of the nodal distance from binary phylogenetic trees to binary phylogenetic networks has the same separation power as the one given in [8].

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Baroni, M., Semple, C., Steel, M.: Hybrids in real time. Syst. Biol. 55, 46–56 (2006)

    Article  Google Scholar 

  2. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: A distance metric for a class of tree-sibling phylogenetic networks. Bioinformatics 24, 1481–1488 (2008)

    Article  Google Scholar 

  3. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: Metrics for phylogenetic networks I: Generalizations of the Robinson-Foulds metric. IEEE T. Comput. Biol. 6, 1–16 (2009)

    Article  Google Scholar 

  4. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: Metrics for phylogenetic networks II: Nodal and triplets metrics. IEEE T. Comput. Biol. 6, 454–469 (2009)

    Article  Google Scholar 

  5. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: On Nakhleh’s metric for reduced phylogenetic networks. IEEE T. Comput. Biol. 6, 629–638 (2009)

    Article  Google Scholar 

  6. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: Comparison of galled trees. IEEE T. Comput. Biol. (in press, 2010)

    Google Scholar 

  7. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: Nodal distances for rooted phylogenetic trees. J. Math. Biol. (in press, 2010)

    Google Scholar 

  8. Cardona, G., Llabrés, M., Rosselló, F., Valiente, G.: Path lengths in tree-child time consistent hybridization networks. Information Sciences 180, 366–383 (2010)

    Article  MATH  Google Scholar 

  9. Cardona, G., Rosselló, F., Valiente, G.: Comparison of tree-child phylogenetic networks. IEEE T. Comput. Biol. 6, 552–569 (2009)

    Article  Google Scholar 

  10. Gusfield, D., Eddhu, S., Langley, C.H.: Optimal, efficient reconstruction of phylogenetic networks with constrained recombination. J. Bioinform. Comput. Biol. 2(1), 173–213 (2004)

    Article  Google Scholar 

  11. Jin, G., Nakhleh, L., Snir, S., Tuller, T.: Maximum likelihood of phylogenetic networks. Bioinformatics 22(21), 2604–2611 (2006)

    Article  Google Scholar 

  12. Moret, B.M.E.: Computational challenges from the tree of life. In: Demetrescu, C., Sedgewick, R., Tamassia, R. (eds.) Proc. 7th Workshop Algorithm Engineering and Experiments and 2nd Workshop Analytic Algorithmics and Combinatorics, pp. 3–16. SIAM, Philadelphia (2005)

    Google Scholar 

  13. 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 T. Comput. Biol. 1, 13–23 (2004)

    Article  Google Scholar 

  14. Nakhleh, L.: Phylogenetic networks. Ph.D. thesis, University of Texas at Austin (2004)

    Google Scholar 

  15. Nakhleh, L.: A metric on the space of reduced phylogenetic networks. IEEE T. Comput. Biol. (in press, 2010)

    Google Scholar 

  16. Nakhleh, L., Warnow, T., Linder, C.R., John, K.S.: Reconstructing reticulate evolution in species: Theory and practice. J. Comput. Biol. 12(6), 796–811 (2005)

    Article  Google Scholar 

  17. Page, R.D.M.: Phyloinformatics: Toward a phylogenetic database. In: Wang, J.T.L., Zaki, M.J., Toivonen, H., Shasha, D. (eds.) Data Mining in Bioinformatics, pp. 219–241. Springer, Heidelberg (2005)

    Chapter  Google Scholar 

  18. Rosselló, F., Valiente, G.: All that glisters is not galled. Mathematical Biosciences 221, 54–59 (2009)

    Article  MATH  MathSciNet  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2010 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Cardona, G., Llabrés, M., Rosselló, F. (2010). Two Results on Distances for Phylogenetic Networks. In: Rocha, M.P., Riverola, F.F., Shatkay, H., Corchado, J.M. (eds) Advances in Bioinformatics. Advances in Intelligent and Soft Computing, vol 74. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-13214-8_12

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-13214-8_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-13213-1

  • Online ISBN: 978-3-642-13214-8

  • eBook Packages: EngineeringEngineering (R0)

Publish with us

Policies and ethics