Skip to main content
Springer Nature Link
Log in

An Enhanced Algorithm for Reconstructing a Phylogenetic Tree Based on the Tree Rearrangement and Maximum Likelihood Method

  • Conference paper
  • First Online:
Intelligent Computing Theories and Methodologies (ICIC 2015)

Part of the book series: Lecture Notes in Computer Science ((LNISA,volume 9226))

Included in the following conference series:

  • 1610 Accesses

Abstract

The phylogeny reconstruction problem is a fundamental problem in computational molecular biology and biochemical physics. Since the number of data sets has grown substantially in recent years, the accuracy and speed of constructing phylogenies become increasingly critical. Numerous studies have demonstrated that the maximum likelihood (ML) method is the most effective method for reconstructing a phylogenetic tree from sequence data. Conversely, tree bisection and reconnection (TBR) is a tree topology rearrangement method that can generate an extensive tree space. In this paper, we propose an enhanced method for reconstructing phylogenetic trees in which the TBR operation is modified and combined with the minimum evolution principle to filter out some unnecessary reconnected positions to reduce the search time. The experiment results demonstrate that the proposed method can assist other algorithms in constructing more accurate trees within a reasonable time.

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

Access this chapter

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

Notes

  1. 1.

    In a graph G, the subdivision of an edge (x, y) by a node z involves replacing (x, y) with a path 〈x, z, y〉 through a new node z.

  2. 2.

    NNI is a local tree rearrangement method that generates two alternative trees by swapping a subtree on one side of the branch with a subtree on the other side.

References

  1. Baba, M.L., Darga, L.L., Goodman, M., Czelusniak, J.: Evolution of cytochrome C investigated by the maximum parsimony method. J. Mol. Evol. 17, 197–213 (1981)

    Article  Google Scholar 

  2. Bordewich, M., Gascuel, O., Huber, K.T., Moulton, V.: Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans. Comput. Biol. Bioinf. 6, 110–117 (2009)

    Article  Google Scholar 

  3. Bordewich, M., Semple, C.: On the computational complexity of the rooted subtree prune and regraft distance. Ann. Comb. 8, 409–423 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  4. Brent, R.: Algorithms for Minimization Without Derivatives. Prentice Hall Inc., Englewood Cliffs (1973)

    MATH  Google Scholar 

  5. Bryant, D.: The splits in the neighborhood of a tree. Ann. Comb. 8, 1–11 (2004)

    Article  MathSciNet  MATH  Google Scholar 

  6. Culik II, K., Wood, D.: A note on some tree similarity measures. Inf. Process. Lett. 15, 39–42 (1982)

    Article  MATH  Google Scholar 

  7. Day, W.H.E.: Properties of the nearest neighbor interchange metric for trees of small size. J. Theor. Biol. 101, 275–288 (1983)

    Article  Google Scholar 

  8. Edwards, A.W.F., Cavalli-Sforza, L.L.: The reconstruction of evolution. Ann. Hum. Genet. 27, 105–106 (1963)

    Google Scholar 

  9. Desper, R., Gascuel, O.: Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J. Comput. Biol. 9, 687–705 (2002)

    Article  Google Scholar 

  10. Felsenstein, J.: Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17, 368–376 (1981)

    Article  Google Scholar 

  11. Fauvel, J.: Algorithms in the pre-calculus classroom: who was Newton- Raphson? Math. Sch. 27, 45–47 (1998)

    Google Scholar 

  12. Felsenstein, J.: Inferring Phylogenies. Sinauer, Sunderland (2004)

    Google Scholar 

  13. Gaut, B.S., Lewis, P.O.: Success of maximum likelihood phylogeny inference in the four-taxon case. Mol. Biol. Evol. 12, 152–162 (1995)

    Article  Google Scholar 

  14. Guindon, S., Gascuel, O.: A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52, 696–704 (2003)

    Article  Google Scholar 

  15. Harper, J.T., Waanders, E., Keeling, P.J.: On the monophyly of chromalveolates using a six-protein phylogeny of eukaryotes. Int. J. Syst. Evol. Microbiol. 55, 487–496 (2005)

    Article  Google Scholar 

  16. Hasegawa, M., Kishino, H., Yano, T.: Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. Evol. 21, 160–174 (1985)

    Article  Google Scholar 

  17. Hordijk, W., Gascuel, O.: Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics 21, 4338–4347 (2005)

    Article  Google Scholar 

  18. Huelsenbeck, J.P., Crandall, K.A.: Phylogeny estimation and hypothesis testing using maximum likelihood. Ann. Rev. Ecol. Syst. 28, 437–466 (1997)

    Article  Google Scholar 

  19. Huelsenbeck, J.F., Hillis, D.M.: Success of phylogenetic methods in the four-taxon Case. Syst. Biol. 42, 247–264 (1993)

    Article  Google Scholar 

  20. Jukes, T.H., Cantor, C.R.: Evolution of protein molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism. Academy Press, New York (1969)

    Google Scholar 

  21. Jones, N.C., Pevzner, P.A.: An Introduction to Bioinformatics Algorithms. The MIT Press, Cambridge (2004)

    Google Scholar 

  22. Ho, C.K., Shuman, S.: Trypanosoma brucei RNA triphosphatase: antiprotozoal drug target and guide to eukaryotic phylogeny. J. Biol. Chem. 276, 46182–46186 (2001)

    Article  Google Scholar 

  23. Jiang, H., Blouin, C.: Insertions and the emergence of novel protein structure: a structure-based phylogenetic study of insertions. BMC Bioinf. 8, 444–458 (2007)

    Article  Google Scholar 

  24. Kimura, M.: A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J. Mol. Evol. 16, 111–120 (1980)

    Article  Google Scholar 

  25. Kuhner, M.K., Felsenstein, J.: A simulation comparison of phylogeny algorithms under equal and unequal evolutionary rates. Mol. Biol. Evol. 11, 459–468 (1994)

    Google Scholar 

  26. Keane, T.M., Naughton, T.J., Travers, S.A.A., Mclnerney, J.O., McCormack, G.P.: DPRml: distributed phylogeny reconstruction by maximum likelihood. Bioinformatics 21, 969–974 (2005)

    Article  Google Scholar 

  27. Lamboy, W.F.: The accuracy of the maximum parsimony method for phylogeny reconstruction with morphological characters. Syst. Bot. 19, 189–505 (1994)

    Article  Google Scholar 

  28. Larget, B., Simon, D.L.: Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees. Mol. Biol. Evol. 16, 750–759 (1999)

    Article  Google Scholar 

  29. Ledford, R.M.: VP1 sequencing of all human rhinovirus serotypes: insights into genus phylogeny and susceptibility to antiviral capsid-binding compounds. J. Virol. 78, 3663–3674 (2004)

    Article  Google Scholar 

  30. Lemey, P., Pybus, O.G., Wang, B., Saksena, N.K., Salemi, M., Vandamme, A.M.: Tracing the origin and history of the HIV-2 epidemic. Nat. Acad. Sci. 100, 6588–6592 (2003)

    Article  Google Scholar 

  31. Lemmon, A., Milinkovitch, M.: The metapopulation genetic algorithm: an efficient solution for the problem of large phylogeny estimation. Nat. Acad. Sci. US Am. 99, 10516–10521 (2002)

    Article  Google Scholar 

  32. Ludwig, W.: ARB: a software environment for sequence data. Nucleic Acids Res. 32, 1363–1371 (2004)

    Article  Google Scholar 

  33. Mau, B., Newton, M.A., Larget, B.: Bayesian phylogenetic inference via Markov Chain Monte Carlo methods. Biometrics 55, 1–12 (1999)

    Article  MathSciNet  MATH  Google Scholar 

  34. Michener, C., Sokal, R.: A quantitative approach to a problem in classification. Evolution 11, 130–162 (1957)

    Article  Google Scholar 

  35. Neyman, J.: Statistical Decision Theory and Related Topics. Academy Press, New York (1971)

    Google Scholar 

  36. Ohkuma, M., Saita, S., Inoue, T., Kudo, T.: Comparison of four protein phylogeny of parabasalian symbionts in termite guts. Mol. Phylogenet. Evol. 42, 847–853 (2007)

    Article  Google Scholar 

  37. Ranwez, V., Gascuel, O.: Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets. Mol. Biol. Evol. 19, 1952–1963 (2002)

    Article  Google Scholar 

  38. Rosenberg, M., Kumar, S.: Traditional phylogenetic reconstruction methods reconstruct shallow and deep evolutionary relationships equally well. Mol. Biol. Evol. 18, 1823–1827 (2001)

    Article  Google Scholar 

  39. Saitou, N., Nei, M.: The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4, 406–425 (1987)

    Google Scholar 

  40. Song, Y.S.: Properties of subtree-prune-and-regraft operations on totally-ordered phylogenetic trees. Ann. Comb. 10, 147–163 (2006)

    Article  MathSciNet  MATH  Google Scholar 

  41. Stamatakis, A., Ludwig, T.: RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees. Bioinformatics 21, 456–463 (2005)

    Article  Google Scholar 

  42. Stamatakis, A., Hoover, P., Rougemont, J.: A rapid bootstrap algorithm for the RAxML web servers. Syst. Biol. 75, 758–771 (2008)

    Article  Google Scholar 

  43. Takezaki, N., Nei, M.: Inconsistency of the maximum parsimony method when the rate of nucleotide substitution is constant. J. Mol. Evol. 39, 210–218 (1994)

    Google Scholar 

  44. Winkworeth, R.C., Bryant, D., Lockhart, P.J., Havell, D., Moulton, V.: Biogeographic interpretation of splits graph: least squares optimization of branch length. Syst. Biol. 54, 56–65 (2005)

    Article  Google Scholar 

  45. Yang, Z., Rannala, B.: Bayesian phylogenetic Inference using DNA sequences: a Markov Chain Monte Carlo method. Mol. Biol. Evol. 14, 717–724 (1997)

    Article  Google Scholar 

  46. Yang, Z.: Computational Molecular Evolution. Oxford University Press, Oxford (2006)

    Book  Google Scholar 

  47. http://www.ncbi.nlm.nih.gov/genbank/

Download references

Author information

Authors and Affiliations

  1. Department of Computer Science and Information Engineering, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan

    Sun-Yuan Hsieh, Hao-Che Hung, Yi-Chun Chen & Chia-Wei Lee

  2. Institute of Medical Informatics, National Cheng Kung University, No. 1, University Road, Tainan, 701, Taiwan

    Sun-Yuan Hsieh & I-Pien Tsai

  3. Department of Information Management, Chang Jung Christian University, No.1, Changda Road, Gueiren District, Tainan, 711, Taiwan

    Hsin-Hung Chou

Authors
  1. Sun-Yuan Hsieh
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. I-Pien Tsai
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Hao-Che Hung
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Yi-Chun Chen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Hsin-Hung Chou
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Chia-Wei Lee
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Sun-Yuan Hsieh .

Editor information

Editors and Affiliations

  1. Tongji University, Shanghai, China

    De-Shuang Huang

  2. University of Ulsan, Ulsan, Korea (Republic of)

    Kang-Hyun Jo

  3. Liverpool John Moores University, Liverpool, United Kingdom

    Abir Hussain

Rights and permissions

Reprints and permissions

Copyright information

© 2015 Springer International Publishing Switzerland

About this paper

Cite this paper

Hsieh, SY., Tsai, IP., Hung, HC., Chen, YC., Chou, HH., Lee, CW. (2015). An Enhanced Algorithm for Reconstructing a Phylogenetic Tree Based on the Tree Rearrangement and Maximum Likelihood Method. In: Huang, DS., Jo, KH., Hussain, A. (eds) Intelligent Computing Theories and Methodologies. ICIC 2015. Lecture Notes in Computer Science(), vol 9226. Springer, Cham. https://doi.org/10.1007/978-3-319-22186-1_53

Download citation

  • DOI: https://doi.org/10.1007/978-3-319-22186-1_53

  • Published:

  • Publisher Name: Springer, Cham

  • Print ISBN: 978-3-319-22185-4

  • Online ISBN: 978-3-319-22186-1

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics