For pairwise alignment you could use the exact algoritms of
Smith-Waterman (finds best local alignment)
Needleman-Wunch (global alignment)
both available in the free EMBOSS package.
Or the heuristic (very fast but not guaranteed to find the best
alignment) BLAST or FASTA. You can get the blastprogram from NCBI.
You definitely should not use clustalx for pairwise alignment.
Peter Frank wrote:
> I like the output format options of ClustalX. I have used it for
> multiple alignments several times. What I would like to know is
> whether it can also be used for pairwise alignments?
>> I know it is technically possible but are the results any good. Or are
> there any better pairwise alignment programs available? I would much
> prefer it to be offline software like ClustalX rather than online