Hello, I would like to perform a pairwise alignment between 100 samples that each contain about 2,000 sequences from different genomic regions. What I would like is the percent identity (ID) at each of the 2,000 sequences between the 100 samples and a reference set of 2,000 sequences (total of 200,000 % ID values). Are there any recommended programs to perform this large batch of alignments while extracting the % ID or number of similar/different bases?
Thanks,
Ryan
Thanks,
Ryan
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