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.
Thank you. Which version of SILVA would you recommend for classification with Greengene2?
They’re separate databases. I’d use the latest version of our SILVA reference alignment for aligning sequences with align.seqs. If you want to use greengenes2 for classification then you would do that in classify.seqs.
Pat