Write a file called clustalw-mpi.pbs (shown below). Then use the qsub command:
qsub -v file=filename clustalw-mpi.pbs
#!/bin/sh
#PBS -l nodes=1:ppn=8
source /usr/modules/init/bash
module load openmpi openmpi-apps/1.6.4/clustalw
mpirun clustalw-mpi myfile -outfile=myfile.aln -type=protein -align