Open in a separate window. Introduction Recent advances in modern sequencing technologies have resulted in an increasing capability for gathering large data sets. Model selection in phylogenetics. Speed-ups obtained with the shared memory version of ProtTest 3 according to the numbers of threads used in a core shared memory node 4 hexa-core Intel Xeon E processors with 12GB memory. In a system with distributed memory like an cluster, the application scaled well up to 56 processors Fig. National Center for Biotechnology Information , U. 
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Statistical model selection can be a very intensive task when the alignments are large and include divergent sequences, highlighting the need for new bionformatic tools capable of exploiting the available computational resources. Performance Evaluation In order to benchmark the performance of ProtTest 3, we computed the running times for the estimation of the likelihood scores of all candidate models from several real and simulated protein alignments Table 1.
This version, called ProtTest 3, includes new features and extended capabilities. This problem was solved with the hybrid memory approach. The use of ProtTest 3 results in significant performance gains, with observed speedups of up to on a high performance cluster.
ProtTest 3: fast selection of best-fit models of protein evolution
An industry-standard API for shared-memory programming. J Parallel Distr Com. Please review our proftest policy. Indeed, during the last years HPC facilities have become part of the general services provided by prottesf universities and research centers. Moreover, ProtTest 3 includes a number of new and more comprehensive features that significantly extend the capabilities of the previous version: In this case, the scalability went beyond the previous limit, reaching up to in the most complex cases with 8-core nodes Figure 3.
Support Center Support Center. Speed-ups obtained with the distributed memory version of ProtTest 3 according to the numbers of cores used in protetst node cluster with 22.4 quad-core Intel Harpertown processors and 8GB memory per node.
Recent advances in modern sequencing technologies have resulted in an increasing capability for gathering large data sets. We implemented several parallel strategies as distinct execution modes in order to make an efficient use of the different computer architectures that a user might encounter:. In column SizeN indicates the number of sequences and L the length of the alignment.
Selection of best-fit models of protein evolution. In this regard, High Performance Computing HPC becomes essential for the feasibility of more sophisticated —and often more accurate— analyses. The program ProtTest Abascal et al. We implemented several parallel strategies as distinct execution modes in order to make an efficient use of the different computer architectures that a user might encounter: Table 1 Real and simulated alignments used to benchmark ProtTest 3 performance.
Nested parallelism for multi-core HPC systems using Java.
ProtTest 3: fast selection of best-fit models of protein evolution
Author information Copyright and License information Disclaimer. Prottest 3 The general structure and the Java code of ProtTest has been protttest redesigned from a computer engineering point of view. Real and simulated alignments used to benchmark ProtTest 3 performance. Speed-ups obtained with the hybrid memory version of ProtTest 3 according to the numbers of cores used in a node cluster with 2 quad-core Intel Harpertown processors and 8GB memory per node.
Availability ProtTest 3 source code and binaries are freely available under GNU license for download from http: National Center for Biotechnology Information 2.4, U.
Supplementary Material Supplementary information: In order to benchmark the performance of ProtTest 3, we computed the running times for the estimation of the likelihood scores of all candidate models from several real and simulated protein alignments Table 1.
Model selection in phylogenetics. Author manuscript; available in PMC Jan 6. Base tree is the tree used for model likelihood optimization and Seq. Introduction Recent advances in modern protgest technologies have resulted in an increasing capability for prottrst large data sets.
Diego Darriba1, 2 Guillermo L. Speed-ups obtained with the shared memory version of ProtTest 3 according to the numbers of threads used in a core shared memory node 4 hexa-core Intel Xeon E processors with 12GB memory.
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