25. Phylogenetic Search Algorithms for Maximum Likelihood

  1. Mourad Elloumi2 and
  2. Albert Y. Zomaya3
  1. Alexandros Stamatakis

Published Online: 23 DEC 2010

DOI: 10.1002/9780470892107.ch25

Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications

How to Cite

Stamatakis, A. (2011) Phylogenetic Search Algorithms for Maximum Likelihood, in Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications (eds M. Elloumi and A. Y. Zomaya), John Wiley & Sons, Inc., Hoboken, NJ, USA. doi: 10.1002/9780470892107.ch25

Editor Information

  1. 2

    Unit of Technologies of Information and Communication (UTIC) and University of Tunis-El Manar, Tunisia

  2. 3

    School of Information Technologies, The University of Sydney, Australia

Author Information

  1. The Exelixis Lab, Department of Computer Science, Technische Universität München, Germany

Publication History

  1. Published Online: 23 DEC 2010
  2. Published Print: 18 JAN 2011

ISBN Information

Print ISBN: 9780470505199

Online ISBN: 9780470892107

SEARCH

Keywords:

  • phylogeny reconstruction - phylogenetic search algorithms for maximum likelihood;
  • subtree pruning and re-grafting (SPR) - systematic application of SPR, moving to all possible subtrees in a given tree, an SPR or rearrangement cycle;
  • search algorithm design - taking actual alignment shapes into account

Summary

This chapter contains sections titled:

  • Introduction

  • Computing the Likelihood

  • Accelerating the PLF by Algorithmic Means

  • Alignment Shapes

  • General Search Heuristics

  • Computing the Robinson Foulds Distance

  • Convergence Criteria

  • Future Directions

  • References