mothur

Aligned SILVA vs unaligned RDP

Hi all, apologies if this has already been asked here before, but why is the Mothur-formated SILVA database provided with the aligned sequences, while the RDP just has the unaligned sequences? I haven’t seen anything in the manual about recommended ways of generating an RDP alignment. Any insight would be helpful!

Thanks in advance!

The RDP alignment is pretty awful - they don’t try to align the variable regions. It’s not appropriate for alignments. The only reference alignment we encourage people to use is the SILVA reference. That being said, depending on your question, RDP, Silva, and greenegenes all have references that would be good for classification.

Pat