Recently, I am working on clustering amino acid sequences to predict OTU table, with mothur. Now that I know that we cannot use unique.seqs() to deal with amino acid sequences but I do know that once I get the distances between samples, then I can use the following code to realize my goal. Therefore, I am trying to find a way to calculate distances between protein sequences. I wonder if anyone here who has tried to do the same thing could share any experience?
Any kind help will be genuinely appreciated!