|MAFFT: Multiple sequence alignment by fast fourier transformation|
MAFFT is a recent multiple sequence alignment program with the ability to align 1000's of sequences by Fast Fourier Transformation. It can alternatively use an iterative refinement alignment procedure for smaller, more difficult datasets.
Using MAFFT on HPC
Program documentation is available through the home page and through the Marine Biological Laboratory's Workshop on Molecular Evolution. In particular see the algorithm and the program Manual page at MAFFT's home site to maximize MAFFT accuracy.