MAFFT

Overview

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 <∼30,000 sequences), etc. Versions 7.505 with and without extensions are available.

Restrictions on use

There are no restrictions on accessing this software on the CSF. The MAFFT without-extensions version is released under the . Please review the various MAFT with-extensions licenses – this version of the app contains other public domain source codes which have their own licenses.

Please cite your usage of this software using the information at the MAFFT References page.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/intel-19.1/mafft/7.505       # Without extensions version
module load apps/intel-19.1/mafft/7.505-ext   # With extensions version

Running the application

Please do not run MAFFT on the login node. Jobs should be submitted to the compute nodes via batch. For hints and tips on running MAFFT please see their MAFFT – tips page.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

module load apps/intel-19.1/mafft/7.505

mafft --thread $NSLOTS args ...

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission