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  • Staden package - sequence handling and analysis software developed at the Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
  • fasta2 and fasta3 - The FASTA programs find regions of local or global (new) similarity between Protein or DNA sequences (not sure how they are licensed)
  • NCBI-BLAST and other tools - The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences.
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