MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
module spider mafft to find out what environment modules are available for this application.
- HPC_MAFFT_DIR - installation directory
MAFFT is compiled to run on multiple cores, use the --thread <cores> option to specify the number of cores to use. Make sure that this number corresponds to the resources requested in your #PBS -l nodes=1:ppn=<cores> statement.