Parallel sequence alignment using BLAST, the Swift parallel scripting system, and split and merge tools from Caltech.
Example of workflow invocation:
$ swift -config swift.conf blast.swift -d=testDB -i=sequence.seq -n=64
This uses the fastasplitn and blastmerge tools from David Mathog's parallelblast package:
http://saf.bio.caltech.edu/pub/software/molbio/parallelblast_2.0.9.tar.gz
Reference:
David R. Mathog. Parallel BLAST on split databases. Bioinformatics (2003) 19(14): 1865-1866. doi:10.1093/bioinformatics/btg250.