Can you use the same dataset for both the align.seqs command and the classify.seqs? What is the best option for eukaryotic data? To this point, I think that the latest SILVA reference set (silva.nr_v132.align) is the best, but I am not totally sure. Also, do I need to customize this in some way?
The only database you should use for aligning is the SILVA reference. Any of the three databases will work for classification; however, the RDP does not have eukaryotic sequences. For aligning the SILVA eukaryotic dataset, you’ll want to go back over the README to make sure that it works well for the region you have sequenced.