Clustal Omega was developed by the Higgins lab in Dublin. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Set up a batch script along the following lines:
#!/bin/bash #PBS -N ClustalO #PBS -m be module load clustalo cd /data/user/mydir clustalo -i myseqs.fasta --auto
Submit this job with:
qsub -l nodes=1 myjob.batThe above command will submit the job to a default node with 2 cpus. By default, Clustal Omega will use all the cores available on the allocated node. To submit to a node with 4 cores, use:
qsub -l nodes=1:c4 myjob.bat
Type 'freen' to see the available node types and number of cores on each.
Benchmarks: An input file with 630 globin sequences in fasta format took about 28 seconds on a 4-core node.