alteRNA is an alternative to many RNA folding methods. It takes an RNA sequence and computes its single secondary structure. Using dynamic programming, it minimizes a linear combination of energy density and the total free energy.

inteRNA predicts the joint secondary structure of two RNA sequences.

piRNA predicts the joint partition function, equilibrium concentration, ensemble energy, and melting temperature for two RNA sequences.

pRuNA is a sequence based pruning technique that eliminates a significant fraction of a Non coding RNA (ncRNA) data set and retains only the most likely ncRNA candidates for forming a stable joint structure with the query mRNA.

smyRNA is a platform independent C program aiming to discover novel ncRNAs in a given genome using previously annotated ncRNAs.