the questions may sound obvious, but I am having difficulties to find a technique on how to customize the original fasta file of SILVA database that contains Archaea, Bacteria and Eukaryota to get three fasta file for each Domain (for instance here the newer release of SILVA 132). Thereafter, I would like to build files https://mothur.org/wiki/Silva_reference_files such as described here in the release 102 where for each domain I would obtain an 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).
I apologize it may sound simple, but any help would be highly appreciated!