How can I align more than 2 sequences locally (Local Multiple alignment)?

Question

[ehsansepahi]

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?

Answer 1

[Mo]

@ehsansepahi

Here you can find a list of different alignment methods online

http://www.expasy.org/genomics/sequence_alignment or http://molbiol-tools.ca/Alignments.htm

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