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AxML: a fast program for sequential and parallel phylogenetic tree calculations based on the maximum likelihood

Alexandros P Stamatakis1, Thomas Ludwig, Harald Meier

  • 1Department of Computer Science, Technical University of Munich, Institut für Informatik/SAB TU München, Germany. stamatak@in.tum.de

Proceedings. IEEE Computer Society Bioinformatics Conference
|April 20, 2005
PubMed
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Calculating optimal phylogenetic trees using maximum likelihood is computationally intensive. This study introduces AxML, a program with an accelerated topology evaluation function, improving runtime by 35-47% for phylogenetic analysis.

Area of Science:

  • Computational Biology
  • Bioinformatics
  • Evolutionary Biology

Background:

  • Phylogenetic tree reconstruction is crucial for understanding evolutionary relationships.
  • Maximum likelihood methods are widely used but computationally expensive, particularly for large datasets.
  • Existing algorithms often bottleneck on tree evaluation and branch length optimization.

Purpose of the Study:

  • To develop and present AxML, a novel program designed to accelerate the calculation of optimal phylogenetic trees.
  • To introduce algorithmic optimizations for the tree topology evaluation function applicable to various phylogenetic programs.
  • To demonstrate the effectiveness of these optimizations in reducing computation time for phylogenetic analysis.

Main Methods:

  • AxML was developed by modifying the fastDNAml program, incorporating a significantly faster topology evaluation function.

Related Experiment Videos

  • Algorithmic optimizations were designed for general applicability to both sequential and parallel phylogeny programs.
  • The optimized function was integrated into three existing phylogenetic programs to assess its impact.

    • Main Results:

    • The integration of the optimized topology evaluation function led to substantial runtime improvements.
    • Experimental results showed a global runtime improvement ranging from 35% to 47% across different test sets and program versions.
    • These improvements were observed on conventional processor architectures.

    Conclusions:

    • The introduced algorithmic optimizations provide a general and effective approach for accelerating phylogenetic tree calculations.
    • AxML and the integrated optimizations offer a significant speedup for maximum likelihood-based phylogenetic analyses.
    • The findings suggest broader applicability of these optimizations in computational phylogenetics.