Clustal W and Omega of EBI and Blast of NCBI, both globally align sequences. Smith waterman of EBI align sequences locally, but work with just two sequences. I tried some other tools but they align globally. How can I align more than 2 sequences locally?
@ehsansepahi here you can find a list of different alignment methods online
for example you can use DIALIGN
You can have the python code to do pairwise alignment here Pariwise Local And Global Alignment
Here you can find a list of most of available methods http://en.wikipedia.org/wiki/List_of_sequence_alignment_software Just read the description for your use