ProDA is public domain software for multiple alignment of protein sequences with repeated and shuffled elements

ProDA source code can be downloaded here
Benchmarking dataset, testing scripts, and testing results can be downloaded here

ProDA should be cited as:
Phuong T.M., Do C.B., Edgar R.C., and Batzoglou S. Multiple alignment of protein sequences with repeats and rearrangements. Nucleic Acids Research 2006 34(20), 5932-8632

The ProDA algorithm was developed by Tu Minh Phuong, Chuong Do, Robert Edgar, and Serafim Batzoglou