Hi
Current SILVA reference alignment files on Mothur site are from database version 102 which is over a year old by now (Feb 2010). Newest SILVA SSURef (ver 108) contains more than 100k extra sequences. Is there a plan to update these reference alignment files on this site or may I use the latest dataset from SILVA on our environmental samples although it contains both bacterial and eucaryotic references?
Thank you and keep up the good work!
I’m also curious about this.
Thanks
Yeah, there’s a plan 
I need to update the RDP database as well so hopefully we’ll get something up before the next release.
when will the new refernce file be avaiable? I am analyzing an Archaea data and there’s huge number of unclassied sequences, even the classifed ones are not well defined (only in the class level). I wonder weather its caused by the old silva reference or other reasons. Can a new reference be the solution? How can I use the downloaded SSURef_111_SILVA_04_08_12_opt in mothur? It’s really urgent for me. Thanks.
Now is already Silva SSU Ref v111 out. Can we expect a new mothur compatible Silva reference alignment soon?
I would also be very interested in updated SILVA files for mothur. Would it be possible to tell us if there is an ETA for a new version of the files? Just so that I can decide if it makes sense to wait with this part of my analysis a bit and use the new files or go on using the old files and somehow deal with all the unclassified sequences. Thanks!