Older version of dist.seqs

Hi all,

I used an older version of mothur (circa 1.6) to generate a distance matrix for a set of amino acid sequences followed by a farthest neighbor clustering command. While I know now that this is not kosher, at the time, it seemed to work for that dataset. Recently, I took the same amino acid alignment, ran it through phylip’s protdist, and then put that into the mothur (v. 1.16) clustering pipeline (Still farthest neighbor). I ended up with the exact same clustering as I did with mothur 1.6. Did older versions of mothur allow clustering of amino acid sequences using some default version of the PROTDIST algorithm? Any idea how this happened?

Weird. No, we’ve never supported amino acid sequences. Anything that’s not an ATG or C would be turned into an N and ignored.