[https://mafft.cbrc.jp/alignment/software/ 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. == Single node == MAFFT can benefit from multiple cores on a single node. For more information: https://mafft.cbrc.jp/alignment/software/multithreading.html '''Note''': The MAFFT_TMPDIR is set to $SLURM_TMPDIR/maffttmp when you load the module. {{File |name=mafft_submit.sh |lang="bash" |contents= #!/bin/bash #SBATCH --time=24:00:00 #SBATCH --nodes=1 #SBATCH --cpus-per-task=32 #SBATCH --mem=0 module load gcc/9.3.0 mafft mafft --globalpair --thread $SLURM_CPUS_PER_TASK input > output }} == Multiple nodes (MPI) == MAFFT can use MPI to align a large number of sequences: https://mafft.cbrc.jp/alignment/software/mpi.html '''Note''': MAFFT_TMPDIR is set to $SCRATCH/maffttmp when you load the module. If you change this temporary directory, it must be shared by all hosts. {{File |name=mafft_mpi_submit.sh |lang="bash" |contents= #!/bin/bash #SBATCH --time=04:00:00 #SBATCH --nodes=2 #SBATCH --ntasks-per-node=4 #SBATCH --cpus-per-task=1 #SBATCH --mem=12G module load gcc/9.3.0 mafft-mpi srun mafft --mpi --large --globalpair --thread $SLURM_CPUS_PER_TASK input > output }}