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A state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. MSAProbs can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input datasets. MSAProbs-MPI is a distributed-memory parallel version of the multithreaded MSAProbs tool that is able to reduce runtimes by exploiting the compute capabilities of common multicore CPU clusters. Our performance evaluation on a cluster with 32 nodes (each containing two Intel Haswell processors) shows reductions in execution time of over one order of magnitude for typical input datasets. Furthermore, MSAProbs-MPI using eight nodes is faster than the GPU-accelerated QuickProbs running on a Tesla K20.

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MSAProbs-MPI forum

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MSAProbs-MPI classification

MSAProbs-MPI specifications

Unique identifier:
OMICS_00980
Interface:
Command line interface
Operating system:
Unix/Linux
Parallelization:
MPI
Version:
0.9.7
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Programming languages:
C++
Computer skills:
Advanced
Stability:
Stable

MSAProbs-MPI distribution

versioning

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MSAProbs-MPI support

Maintainer

  • Liu Yongchao <>

Credits

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Publications

Institution(s)

Grupo de Arquitectura de Computadores, Universidade da Coruña, Campus de Elviña, Coruña, Spain; School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, GA, USA; Institut für Informatik, Johannes Gutenberg Universität Mainz, Mainz, Germany

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