Smith-Waterman database searches with inter-sequence SIMD parallelisation
SWIPE is a tool for performing rapid local alignment searches in amino acid or nucleotide sequence databases. It is a highly optimized implementation of the Smith-Waterman algoritm using SIMD parallel computing technology available on common CPUs.
The method and a performance evaluation is described in detail the following publication:
Rognes T (2011)
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation.
BMC Bioinformatics 12, 221. doi:10.1186/1471-2105-12-221
More information about SWIPE can be found on its website.
SWIPE may be installed with Homebrew using the following command:
brew install brewsci/bio/swipe