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Related Experiment Videos

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees.

A Stamatakis1, T Ludwig, H Meier

  • 1Department of Computer Science, Technical University of Munich Boltzmannstrasse 3, D-85748 München, Germany. stamatak@cs.tum.edu

Bioinformatics (Oxford, England)
|December 21, 2004
PubMed
Summary

RAxML-III significantly speeds up the computation of large evolutionary trees using maximum likelihood inference, enabling the analysis of 1,000-taxon trees on a single PC. This open-source program outperforms existing methods on real data for phylogenetic tree reconstruction.

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Bioinformatics (Oxford, England)·2018

Area of Science:

  • Computational Biology
  • Evolutionary Biology
  • Bioinformatics

Background:

  • Statistical phylogenetic models (maximum likelihood, Bayesian inference) are computationally intensive for large datasets.
  • Previous methods limited phylogenetic tree computation to approximately 100 taxa on standard workstations.
  • Accurate phylogenetic tree reconstruction is crucial for understanding evolutionary relationships.

Purpose of the Study:

  • To introduce RAxML-III, a new program for rapid maximum likelihood-based inference of large evolutionary trees.
  • To demonstrate the capability of RAxML-III to compute 1,000-taxon trees efficiently.
  • To compare RAxML-III's performance against other leading phylogenetic inference programs.

Main Methods:

  • Development and implementation of RAxML-III for maximum likelihood phylogenetic inference.

Related Experiment Videos

  • Benchmarking RAxML-III against PHYML and MrBayes using both synthetic and real biological data.
  • Evaluation of computational speed and accuracy (final likelihood values) of the compared programs.

    • Main Results:

    • RAxML-III computes 1,000-taxon trees in under 24 hours on a single PC processor.
    • RAxML-III demonstrates superior speed and achieves better likelihood scores than PHYML and MrBayes on real data alignments.
    • While performing comparably on synthetic data, RAxML-III's real-world performance is significantly enhanced.

    Conclusions:

    • RAxML-III offers a substantial advancement in the computational efficiency of phylogenetic tree inference.
    • The program enables the analysis of significantly larger evolutionary trees than previously feasible on standard hardware.
    • RAxML-III is available as open-source software, promoting wider accessibility and further research in phylogenetics.