This project is not active any more, since we failed to get the permit from the Clustal team to distribute our software!
More details about the program can be obtained from our published paper:
Yongchao Liu, Bertil Schmidt, and Douglas L. Maskell:
"MSA-CUDA: multiple sequence alignment on graphics processing units with CUDA".
20th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2009),
2009, 121-128 (BEST PAPER AWARD)