I’m new Mothur user.
I will analyze reads from our Miseq experiment with Mothur. We are studying photosynthetic marine eukariota so amplicons will be 16S from plastid but and I’m not sure about the reference alignment to use.
Reference alignment for 16S is usually from bacteria sequences, however this gene structure is conserved but not identical between bacteria and eukaria (e.g. V6 is lost in eukariota).
What reference alignment can you suggest for my dataset?
thanks in advance