1. GAME: genetic algorithm based motif elicitation
  2. PLAST-ncRNA: Partition function Local Alignment Search Tool for non-coding RNA sequences
  3. Searching for evolutionary distant RNA homologs within large genomic sequences
  4. Recursive-iterative-DCM3 for large scale phylogeny reconstruction
  5. Probalign for multiple sequence alignment
  6. Sdiscover: finding active motifs in a set of protein or DNA sequences
  7. RSmatch/RADAR: aligning RNA secondary structures and finding RNA motifs