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The Basic Local Alignment Search Tool is a widely-used tool for finding and evaluating DNA or protein sequences. Users can utilize either their own sequences or the genomes of hundreds of organisms. It can be found at http://blast.ncbi.nlm.nih.gov/Blast.cgi
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Aligning multiple sequences in heterogeneous group
I tried making a custom BLAST database and then BLASTed each sequence against it, but then I get multiple hits for the same alignment (with the group 2 example above, seq2:seq6, seq2:seq7, seq6:seq2, seq6 …