Advertisement

Mathematical Inference and Application of Expectation-Maximization Algorithm in the Construction of Phylogenetic Tree

  • Kai Yang
  • Deshuang Huang
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7996)

Abstract

The central task in the research of molecular evolution may be the reconstruction of a phylogenetic tree from sequences of taxa. So, phylogenetic tree is also known as the evolutionary tree, which uses a kind of graph similar to the tree branch to represent the genetic relationship among the organisms and infers the evolutionary history of the species based on the study of biological sequences. The result of phylogenetic analysis is usually expressed in the form of phylogenetic tree. This paper makes estimations on the parameters of the phylogenetic tree by EM algorithm to estimate the optimum length of the branch under parameter model to pave the way for constructing a better phylogenetic tree.

Keywords

Mathematical inference EM algorithm Phylogenetic analysis 

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Barbara, E.E., Michael, I.J., Kathryn, E.M.: Protein Molecular Function Prediction by Bayesian Phylogenomics. PLoS Computational Biology 1(5), e45 (2005)CrossRefGoogle Scholar
  2. 2.
    Felsentein, J.: Phy logenies from mo lecular sequences: Inference and Reliability. Annual Review of Genetic 22, 521–565 (1988)CrossRefGoogle Scholar
  3. 3.
    Eisen, J.A., Hanawalt, P.C.: A Phylogenomics Study of DNA Repair Genes, Proteins, and Processes. Mutation Research (3), 171–213 (1999)CrossRefGoogle Scholar
  4. 4.
    Jukes, T., Cantor, C.: Evolution of Protein Molecules. In: Munro, H.N. (ed.) Mammalian Protein Metabolism, vol. 21, p. 132. Academic Press, New York (1969)Google Scholar
  5. 5.
    Li, S., Pearl, D., Doss, H.: Phylogenetic Tree Construction using Markov chain Monte Carlo, 451 (2000)Google Scholar
  6. 6.
    Larget, B., Simon, D.L.: Markov Chain Monte Carlo Algorithms for the Bayesian analysis of Phylogenetic Trees. Mol. Biol. E 16, 750–759 (1999)CrossRefGoogle Scholar
  7. 7.
    Kimura, M.: A Simple Method for Estimating Evolutionary Rates of Base Substitutions through Comparative Studies of Nucleotide Sequences. Journal of Molecular Evolution 16 (1980)Google Scholar
  8. 8.
    Tang, X., Wu, C.: Using EM Algorithm to Estimate Parameters in Phylogenetic Tree Construction. Chinese Journal of Applied Probability and Statistics (2010)Google Scholar
  9. 9.
    Tanner, M.: Tools for Statistical Inference, 3rd edn. Springer, New York (1996)zbMATHCrossRefGoogle Scholar
  10. 10.
    Salter, L., Peal, D.: A Stochastic Search Strategy for Estimation of Maximum Likelihood Phylogenetic Trees (2000)Google Scholar
  11. 11.
    Hostand, O., Bjorklund, M.: Nucloetide Substitution Models and Estimation of Phylogeny. Mol. Biol. E 15, 1381–1389 (1998)CrossRefGoogle Scholar
  12. 12.
    Nei, M., Tajima, F., Tateno, Y.: Accuracy of Estimated Phylogenetic Trees from Molecular Data.II.Gene frequency data. J. Mol. Evol. 19, 153–170 (1983)CrossRefGoogle Scholar
  13. 13.
    Goldman, N.: The Statistical Tests of the Models of the DNA Substitution. J. Mol. E 36, 182–198 (1993)CrossRefGoogle Scholar
  14. 14.
    Li, W.-H.: A Statistical Test of the Phylogenies Estimated from Sequence Data. Mol. Biol. E 6, 424–435 (1989)Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  • Kai Yang
    • 1
  • Deshuang Huang
    • 1
  1. 1.College of Electronic and Information EngineeringTongji UniversityShanghaiChina

Personalised recommendations