How can I align more than 2 sequences locally?
You have to do it pairwise (there is no other option).

You can do that with BLAST or even SSEARCH (Smith-Watermann). If you have a fasta file of your sequences then do this:


make index of your sequences using makeblastdb -dbtype nucl -in &lt;yourfastafile&gt; -out &lt;yourdbindex&gt;
Run BLAST with your &lt;yourfastafile&gt; as input and &lt;yourdbindex&gt; as database with desired parameters. This will do a pairwise alignment between all sequences


Similar strategy can be used for SSEARCH.