To make use of the aligner in mothur, you need a reference database. Here we provide 16S rRNA sequence alignments. If you have a reference alignment that you would like to donate, please add it to the list.
rRNA gene sequences
The greengenes alignment is 7,682 columns long and is basically the alignment that ARB started with. The variable regions could use some improving, but few people get paid enough to do it all themselves. You can download copies of the greengenes-formatted databases.
You can download copies of our attempt to recreate the SILVA SEED databases for the Bacteria, Archaea, and Eukarya