SSalign is a DNA/RNA alignment program. This program was developed due to a need to look at all possible stem-loop structures that a large number of DNA/RNA sequences could form. Aligning each sequence with its reverse using available programs proved not fast enough and quite problematic as extensive post-processing of the results was required to remove redundant and find (and clean) "impossible" alignments.

Requirements:
* Java

The license of this software is Free, you can free download and free use this calculator software.