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I have an MSA from MAFFT (as a FASTA file; there are several sequences in the MSA), and I would like to quantify the "variants" between these sequences.

What is the standard tool to do something like this?

I would prefer to know the non-consensus variants in the the entire MSA, but that may be too tricky, so I would like to figure out the non-consensus variants between those select sequences.

I'm familiar with calculating an MSA, and then visualizing it---but I would like an output file with all of the different bases.

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