Would like to ask if you would recommend doing protozoa assignations with Mothur (SILVA132 database).
I saw some comments in the forum but rise this question, because I was trying with a dataset. Instead of doing a reference alignment, I went for the pre.cluster (alignment=needleman) and after some cleaning (chimera and remove seqs), I asked for the pairwise.seqs to obtain the dist file. My problem is precisely in that last step. It is taking long and many times the process does not continue.
Any suggestion I would really appreciate it,