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. © Springer-Verlag Berlin Heidelberg 2005.
CITATION STYLE
Stamatakis, A., Ott, M., & Ludwig, T. (2005). RAxML-OMP: An efficient program for phylogenetic inference on SMPs. In Lecture Notes in Computer Science (Vol. 3606, pp. 288–302). Springer Verlag. https://doi.org/10.1007/11535294_25
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