The gridaligner is an open source Java implementation of the Smith-Waterman algorithm for biological local pairwise sequence alignment that runs in a distributed environment using the vgrid framework. For aligning, the code of the open source project JAligner is used. Details about the algorithm and its configuration can be found on the JAligner homepage.

URL

http://vgrid.sourceforge.net/gridaligner/

JAligner:
http://jaligner.sourceforge.net