If you are just looking for something the quality of BaliBase, you can make up whatever alignments you like. Balibase is NOT gold-standard quality. It is long past time to discard Balibase and create a better alignment benchmark. Getting reliable nucleotide alignments for protein-coding sequences is not too hard (use a good protein alignment, then look up the original DNA), but for non-coding DNA, getting experimental validation of alignments is extremely difficult. You can get some ribosomal RNA alignments that are pretty good, that use the secondary structure as well as the primary structure in making the alignments. Kevin Karplus karplus at soe.ucsc.edu http://www.soe.ucsc.edu/~karplus life member (LAB, Adventure Cycling, American Youth Hostels) Effective Cycling Instructor #218-ck (lapsed) Professor of Computer Engineering, University of California, Santa Cruz Undergraduate and Graduate Director, Bioinformatics Affiliations for identification only.