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Silva reference files
The SILVA alignment is 50,000 columns long so that it can be compatible with 18S rRNA sequences as well as archaeal 16S rRNA sequences. The actual reference alignment that SILVA uses with their SINA aligner is called the SEED alignment. We don't know what this actually is. We have tried to duplicate it by identifying the unique sequences in the SSURef database (v102) that have a 100% quality score to the SEED alignment and that go from the end of the traditional 8f/27f primer to the beginning of the traditional 1492r primer. We are providing separate datasets for bacterial, archaeal, and eukaryotic sequences. Within each reference set are the aligned sequence file (e.g. silva.bacteria.fasta), an unaligned sequence file (e.g. nogap.bacteria.fasta), and taxonomy outlines (e.g. silva.bacteria.silva.tax):