SmithWaterman-CUDA. The GPGPU project to run Smith-Waterman algorithm on the modern GPU (s) made by NVIDIA
compatible GPU cards as efficient hardware accelerators for
Smith-Waterman sequence alignment", BMC Bioinformatics 2008,
9(Suppl 2):S10 (26 March 2008)
The source code is available here. The last version is swcuda-1.92.tgz. To make it run follow the instructions in the documentation page.
A pre-compiled binary package for Linux Fedora Core 8 is available as well: http://www.manavski.com/downloads/smithwaterman-cuda-fc8-1.84.tgz
For people having other Linux distributions please note the binary is compiled in the following environment: