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
Please see the README and CHANGES file for a little bit of documentation.
More information about SWIPE can be found on its website.