Using mothur for amino acid sequences?

Hello everyone!

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!


Hi Emmett,

You could use something like phylip’s protdist to generate a distance matrix and then feed that into cluster. Sorry we never got very far in developing mothur for protein coding sequences! Maybe we should look at that again.


Thank you! I will try it.

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