This is the Linux app named CUDAlign whose latest release can be downloaded as masa-cudalign-126.96.36.1994.tar.gz. It can be run online in the free hosting provider OnWorks for workstations.
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CUDAlign is a tool able to align pairwise DNA sequences of unrestricted size in CUDA GPUs, using the Smith-Waterman algorithm combined with Myers-Miller. It produces the optimal alignment of 1 million base sequences in 45 seconds using a GTX 560 Ti. Many optimizations are being developed for this software. Look at the following papers for detailed information:
 Edans Sandes, Alba Melo. Retrieving Smith-Waterman Alignments with Optimizations for Megabase Biological Sequences using GPU. IEEE Transactions on Parallel and Distributed Systems, vol. 99, PrePrints, 2012
 Edans Sandes, Alba Melo. Smith-Waterman Alignment of Huge Sequences with GPU in Linear Space. IPDPS 2011: 1199-1211
 Edans Sandes, Alba Melo. CUDAlign: using GPU to accelerate the comparison of megabase genomic sequences. PPOPP 2010: 137-146
The latest source code can be found in Github. See the MASA project at https://github.com/edanssandes/MASA-CUDAlign
Java Swing, Command-line
This is an application that can also be fetched from https://sourceforge.net/projects/cudalign/. It has been hosted in OnWorks in order to be run online in an easiest way from one of our free Operative Systems.