Hello, I performed 16S analysis based on greengenes database version gg_13_8_99, but the reviewer suggested the updated database in greengenes2. I’m not sure that can I get the mothur-compatible version of the latest greengenes.
Thank you very much.
why not Silva? I haven’t looked that closely at greengenes2 but unless you are using the phylogenetic tree part, I’d guess silva is more complete
Let me see what I can do - the formatting doesn’t look to awful, but it might take me a couple of days.
Hey Awil,
Sorry for the delay - I just posted a mothur formatted version of the greengenes2 database. You can find it here:
Be sure to look over the README that is linked in that page for information on how I curated the database. Thanks for pushing me to get it done!
Pat
Hello @pschloss
so thankful to know the way to convert gg2.
I downloaded files and tried align.seqs(fasta=ecoli_V*.fasta, reference=greengenes2.fasta),
but the error comes up like this:
[ERROR]: template is not aligned, aborting.
How can I deal with it?
Thanks!
EY
Thank you in advance for your help. 
It’s not an alignment. It’s only for classification. For alignment you should use the silva reference alignment.