Dear Dr Schloss
I am trying to align few thousand reads using align.seqs command. I want to use silva Bacterial references (14,956 sequences) database as a template alignment.
For using the Greengenes database as template alignment, I can see the core_set_aligned.imputed.fasta when I download the Greengenes.alignment zip file. But when I download the silva Bacterial references and unzip it I do not see and core_set_aligned.imputed.fasta file. I do see some other files such as 1) nogap.bacteria.fasta 2) silva.bacteria.fasta etc.
My question is which one will be used as template alignment out of these files?
Thank you for offering such a wonderful open source program for community analysis.