Aligns and optionally taxonomically classifies ribosomal RNA (rRNA gene sequences). SINA is part of the rRNA gene processing pipeline of the SILVA ribosomal databases project. The software can execute a homology search based on the computed alignment and generate a per sequence classifications from the search results. It also allows to convert reference alignments from FASTA to ARB format. SINA was compared with the commonly used high throughput multiple sequence alignment (MSA) programs PyNAST and mothur.