Code/Tool to locally do sequence alignment

Question

[c_u]

Hi,

I have a sequence (A). And I have a set of hundreds of other sequences; I want to test the sequence similarity of each of these hundreds of sequences to A. Then I will select the ones that are highly similar. I know there are many online tools, like Emboss Needle. But is there a way to do this locally on my system?

[GenoMax]

You can indeed download EMBOSS suite and use Needle locally.

Answer 1

[Ahill]

Yes, you can download, install, and run locally many tools that can match sequences to A. For example, BLAST is available here: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download. The best tool to use would depend on your specific requirements. If you want to do pairwise sequence alignment like Needle does, one alternative would be to download and install ClustalW. Executables available from http://www.clustal.org/clustal2/

Answer 2

[wulj2]

maybe, muscle(https://www.drive5.com/muscle/ )will help you out