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. 2011 Apr 15;27(8):1164-5.
doi: 10.1093/bioinformatics/btr088. Epub 2011 Feb 17.

ProtTest 3: fast selection of best-fit models of protein evolution

Diego Darriba  1 , Guillermo L Taboada, Ramón Doallo, David Posada
Affiliations

ProtTest 3: fast selection of best-fit models of protein evolution

Diego Darriba et al. Bioinformatics. .

Abstract

We have implemented a high-performance computing (HPC) version of ProtTest that can be executed in parallel in multicore desktops and clusters. This version, called ProtTest 3, includes new features and extended capabilities.

Availability: ProtTest 3 source code and binaries are freely available under GNU license for download from http://darwin.uvigo.es/software/prottest3, linked to a Mercurial repository at Bitbucket (https://bitbucket.org/).

Contact: [email protected]

Supplementary information: Supplementary data are available at Bioinformatics online.

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Figures

Figure 1
Figure 1
Speed-ups obtained with the shared memory version of ProtTest 3 according to the numbers of threads used in a 24-core shared memory node (4 hexa-core Intel Xeon E7450 processors) with 12GB memory.
Figure 2
Figure 2
Speed-ups obtained with the distributed memory version of ProtTest 3 according to the numbers of cores used in a 32-node cluster with 2 quad-core Intel Harpertown processors and 8GB memory per node. Up to 4 processes where executed per node because of the memory requirements of the largest datasets (10K, 20K, 100K).
Figure 3
Figure 3
Speed-ups obtained with the hybrid memory version of ProtTest 3 according to the numbers of cores used in a 32-node cluster with 2 quad-core Intel Harpertown processors and 8GB memory per node. Up to 4 MPJ Express processes per node and at least 2 OpenMP threads for each ML optimization were executed.
See this image and copyright information in PMC

References

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