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Smith-Waterman database searches with inter-sequence SIMD parallelisation
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torognes/swipe
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Smith-Waterman database searches with inter-sequence SIMD parallelisation
SWIPE is a tool for performing rapid local alignment searches in amino acidor nucleotide sequence databases. It is a highly optimized implementation ofthe Smith-Waterman algoritm using SIMD parallel computing technology availableon common CPUs.
The method and a performance evaluation is described in detail the followingpublication:
Rognes T (2011)
Faster Smith-Waterman database searches with inter-sequence SIMDparallelisation.
BMC Bioinformatics 12, 221.doi:10.1186/1471-2105-12-221
Please see theREADMEandCHANGES file fora little bit of documentation.
More information about SWIPE can be found on itswebsite.
SWIPE may be installed with Homebrew using the following command:
brew install brewsci/bio/swipe
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Smith-Waterman database searches with inter-sequence SIMD parallelisation