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.


20130301 SWIPE is now available on GitHub. Future versions will be made available there.

20121110 SWIPE version 2.0.5 released. Added option (-H) to show taxid and membership/link bits.

20120704 SWIPE version 2.0.4 released. Fixed bug with display of header lines with TSV format (-m 9).

20120611 SWIPE version 2.0.3 released. Fixed bug relating to option "-c" not being allowed.

20120608 SWIPE version 2.0.2 released. Fixed bug relating to amino acids "JOU*" on non-SSSE3 cpus. Minor output format changes / bug fixes.

20120224 SWIPE version 2.0.1 released. Fixed bug in display of alignment coordinates in XML and TSV formats.

20120201 SWIPE version 2.0 released. This version incorporates a number of new features compared to the initial release, most notably hit statistics, alignments, as well as support for nucleotide sequences, large databases and MPI.

20110601 Paper published in BMC Bioinformatics.

20110411 Score matrix files are now included in the distribution.

20110305 Initial version released.


Source code and Linux 64-bit executables:


Documentation is meagre at the moment, but please see the README and CHANGES file.


Source code and executables for SWIPE is available under the GNU Affero General Public License, version 3.


Rognes T (2011)
Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation
BMC Bioinformatics 12, 221


© 2008-2012 Torbjørn Rognes, University of Oslo, Oslo University Hospital and Sencel Bioinformatics AS.

Updated 10 Nov 2012