Smith-Waterman database searches with inter-sequence SIMD parallelisation
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CHANGES
COPYING
Makefile SWIPE 2.0.9 Jan 21, 2014
README Update README Jan 21, 2014
README.md
align.cc SWIPE 2.0.10 - Fix for non-symmetric matrices Jun 25, 2014
asnparse.cc
blastkar_partial.c
blastkar_partial.h SWIPE version 2.0.5 Dec 5, 2012
database.cc Fix for changes to NCBI database format May 4, 2018
hits.cc Added query description to XML output Nov 13, 2017
matrices.cc
query.cc
scoring.pdf
search16.cc Minor formatting changes to source code Mar 8, 2017
search16s.cc
search63.cc
search7.cc
stats.cc
swipe.cc
swipe.h

README.md

SWIPE

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.

SWIPE may be installed with Homebrew using the following command:

brew install brewsci/bio/swipe