The Silva reference provided in the mothur wiki is as alignment, while the RDP reference is just a fasta file.
If I want to use Silva for classification, should I convert the alignment to an ordinary fasta?
If yes, what is the most convenient tool to do this? Doesn’t work with simplest text file operations, as both the sequence names and the sequences contain dots.
And finally, is it still so that neither Silva or RDP is clearly better for classification, or is the most recent Silva now better?
Sorry for the dumbish questions, I’m still learning…