RAxML-OMP: An Efficient Program for Phylogenetic Inference on SMPs

  • Alexandros Stamatakis
  • Michael Ott
  • Thomas Ludwig
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3606)


Inference of phylogenetic trees comprising hundreds or even thousands of organisms based on the Maximum Likelihood (ML) method is computationally extremely intensive. In order to accelerate computations we implemented RAxML-OMP, an efficient OpenMP-parallelization for Symmetric Multi-Processing machines (SMPs) based on the sequential program RAxML-V (Randomized Axelerated Maximum Likelihood). RAxML-V is a program for inference of evolutionary trees based upon the ML method and incorporates several advanced search algorithms like fast hill-climbing and simulated annealing. We assess performance of RAxML-OMP on the widely used Intel Xeon, Intel Itanium, and AMD Opteron architectures. RAxML-OMP scales particularly well on the AMD Opteron architecture and achieves even super-linear speedups for large datasets (with a length ≥ 5.000 base pairs) due to improved cache-efficiency and data locality. RAxML-OMP is freely available as open source code.


Branch Length Phylogenetic Inference Alignment Length Open Source Code Distribute Shared Memory 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2005

Authors and Affiliations

  • Alexandros Stamatakis
    • 1
  • Michael Ott
    • 2
  • Thomas Ludwig
    • 3
  1. 1.Institute of Computer ScienceFoundation for Research and Technology-HellasHeraklion, CreteGreece
  2. 2.Department of Computer ScienceTechnical University of MunichGarching b. MünchenGermany
  3. 3.Department of Computer ScienceRuprecht-Karls UniversityHeidelbergGermany

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