rDNA Alignment Service
Our ribosomal RNA gene alignment service is intended for large-scale or non-recurring projects. On our computer cluster we can align up to 10 million reads (average length of 500 nuc - e.g. Roche 454) in a single working day according the SILVA reference alignment which covers all three domains of life.
Please feel free to use the 
SILVA web aligner to exemplarily check the quality of the results for subsets of your data (max. 300 sequences per batch).
The service is reasonably priced and the procedure is quite simple:
We just need your unaligned sequences in a multi-fasta file (or multiple of them) and you will get back your aligned sequences in the same format or as an ARB database file.
Of course, we also take care of "small" projects with e.g. 250,000 (1/4 Roche 454 plate) or clearly less sequences.
For more information please contact 
arb(at)ribocon.com