ACOPHY: A Simple and General Ant Colony Optimization Approach for Phylogenetic Tree Reconstruction

  • Huy Q. Dinh
  • Bui Quang Minh
  • Hoang Xuan Huan
  • Arndt von Haeseler
Part of the Lecture Notes in Computer Science book series (LNCS, volume 6234)

Abstract

We introduce ACOPHY, a novel framework to apply Ant Colony Optimization (ACO) for phylogenetic reconstruction. ACOPHY overcomes a main drawback of other attempts to reconstruct phylogenies by defining a compact ACO graph that is nicely coupled with the tree space. The proposed graph allows the ants to walk globally through the tree space. Thus, ACOPHY can be generally applied to all well-known optimality criteria in phylogenetics. We compared ACOPHY with the traditional phylogenetic method PHYLIP and obtained slightly better results. This is promising since our current implementation of ACOPHY is still at the proof of concept stage. We list a number of points where ACOPHY can be improved. Once the improvements are integrated, we hope for competitive performance against other recent phylogenetic inference methods.

Keywords

Phylogenetic reconstruction ant colony optimization 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2010

Authors and Affiliations

  • Huy Q. Dinh
    • 1
    • 2
  • Bui Quang Minh
    • 1
  • Hoang Xuan Huan
    • 3
  • Arndt von Haeseler
    • 1
  1. 1.Center for Integrative Bioinformatics, Vienna, Max F. Perutz LaboratoriesUniversity of Vienna, Medical University of Vienna, University of Veterinary Medicine ViennaAustria
  2. 2.Gregor Mendel Institute of Molecular Plant BiologyAustrian Academy of SciencesViennaAustria
  3. 3.Faculty of Information TechnologyCollege of TechnologyHanoiVietnam

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