Well- Established Bootstrap Algorithms

  IJETT-book-cover  International Journal of Engineering Trends and Technology (IJETT)          
  
© 2018 by IJETT Journal
Volume-65 Number-1
Year of Publication : 2018
Authors : Asmaa Abdel-Kader, Ahmad Moustafa, Ibrahim Elhenawy
DOI :  10.14445/22315381/IJETT-V65P204

Citation 

MLA Style: Asmaa Abdel-Kader, Ahmad Moustafa, Ibrahim Elhenawy "Well- Established Bootstrap Algorithms" International Journal of Engineering Trends and Technology 65.1 (2018): 17-19.

APA Style:Asmaa Abdel-Kader, Ahmad Moustafa, Ibrahim Elhenawy (2018). Well- Established Bootstrap Algorithms. International Journal of Engineering Trends and Technology, 65(1), 17-19.

Abstract
Maximum-Likelihood is considered to be a powerful statistical method for the process of phylogenetic inference from sequence data (DNA & RNA).Unfortunately, the computation power need for carrying out this method is very high. Although there is a continuous advance in the computational tools and the tools for high-performance computing, the process of finding the phylogenetic tree using ML is still problematic due to the burden of bootstrapping process used in the ML method, which requires very high computations. In this paper, we will go through the different methods developed to optimize the process of bootstrapping.

Reference
[1] B.Efron, “Bootstrap Methods: Another Look at the Jackknife BT - Breakthroughs in Statistics: Methodology and Distribution,” S. Kotz and N. L. Johnson, Eds. New York, NY: Springer New York, 1992, pp. 569–593.
[2] J.Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution (N. Y)., vol. 39, no. 4, pp. 783–791, 1985.
[3] M.Hasegawa and H. Kishino, “Accuracies of the simple methods for estimating the bootstrap probability of a maximum-likelihood tree,” 1994.
[4] J.Adachi and M. Hasegawa, “MOLPHY Version 2.3:Programs for Molecular Phylogenetics Based on Maximum Likelihood Jun Adachi and Masami Hasegawa,” Comput. Sci. Monogr., vol. 28, pp. 1–150, 1996.
[5] W.Hordijk and O. Gascuel, “Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood,” Bioinformatics, vol. 21, no. 24, pp. 4338–4347, 2005.
[6] M.Anisimova and O. Gascuel, “Approximate Likelihood-Ratio Test for Branches : A Fast , Accurate , and Powerful Alternative,” vol. 55, no. 4, pp. 539–552, 2006.
[7] S.Guindon, J. F. Dufayard, V. Lefort, M. Anisimova, W. Hordijk, and O. Gascuel, “New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0,” Syst. Biol., vol. 59, no. 3, pp. 307–321, 2010.
[8] B.Q.Minh, M. Anh, T. Nguyen, and A. Von Haeseler, “Ultrafast Approximation for Phylogenetic Bootstrap,” no. March, 2013.
[9] D.T.Hoang, O. Chernomor, A. von Haeseler, B. Q. Minh, and S. V. Le, “UFBoot2: Improving the Ultrafast Bootstrap Approximation. Molecular biology and evolution.,” Mol. Biol. Evol., vol. 35, no. 2, p. msx281, 2017.
[10] D.T.Hoang, L. S. Vinh, T. Flouri, A. Stamatakis, and A. Von Haeseler, “MPBoot : fast phylogenetic maximum parsimony tree inference and bootstrap approximation,” pp. 1–11, 2018.
[11] P.A.Goloboff, J. S. Farris, and K. C. Nixon, “TNT, a free program for phylogenetic analysis,” Cladistics, vol. 24, no. 5, pp. 774–786, 2008.
[12] D.L.Swofford, “PAUP*: phylogenetic analysis using parsimony (* and other methods). Sunderland, MA.” Sinauer Associates, 2002.

Keywords
Bootstrap; phylogenetic analysis; phylogenetic tree.