The AxML program family for maximum likelihood-based phylogenetic tree inference: Research Articles

  • Authors:

  • Alexandros P. Stamatakis;Thomas Ludwig;Harald Meier

  • Affiliations:

  • Technische Universität München, Lehrstuhl für Rechnertechnik und Rechnerorganisation/I10, Boltzmannstr. 3, D-85748 Garching b. München, Germany;Ruprecht-Karls-Universität Heidelberg, Institut für Informatik, Im Neuenheimer Feld 348, D-69120 Heidelberg, Germany;Technische Universität München, Lehrstuhl für Rechnertechnik und Rechnerorganisation/I10, Boltzmannstr. 3, D-85748 Garching b. München, Germany

  • Venue:
  • Concurrency and Computation: Practice & Experience - High Performance Computational Biology
  • Year:
  • 2004

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Abstract

Inference of phylogenetic (evolutionary) trees comprising hundreds or thousands of organisms based on the maximum likelihood criterion is a computationally extremely intensive task. This paper describes the evolution of the AxML program family which provides novel algorithmic as well as technical solutions for the maximum likelihood-based inference of huge phylogenetic trees. Algorithmic optimizations and a new tree building algorithm yield runtime improvements of a factor greater than 4 compared with fastDNAml and parallel fastDNAml, returning equally good trees at the same time. Various parallel, distributed, and Grid-based implementations of AxML give the program the capability to acquire the large amount of required computational resources for the inference of huge high-quality trees. Copyright © 2004 John Wiley & Sons, Ltd.