Hi everyone,
I have downloaded “silva.seed_v119.align” . Can I use it in “align.seqs” and “classify.seqs”? Is it necessary for me to change name as “silva.seed_v119.fasta”? Compared with RDP and gg database,which is better for classifying our sequences?
Thanks 
I have downloaded “silva.seed_v119.align” . Can I use it in “align.seqs” and “classify.seqs”? Is it necessary for me to change name as “silva.seed_v119.fasta”?
you can use the align file as the input to classify.seqs. it automatically degaps the sequences before classifying.
Compared with RDP and gg database,which is better for classifying our sequences?
depends. 
but seriously, it depends on the environment you’re looking at. I think the silva and gg do pretty well for most environments.
Pat
Thank youï¼