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?