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

The MAFFT program can be run by itself or through T-Coffee. It can also be launched as an "external method" by the SeaView editor. It requires FastA format input file(s). Command line help through:

mafft --help

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.