From Bioinformatics.Org Wiki
- caRNAc - RNA secondary structure inference for set of homologous sequences
- ConsInspector - A tool for the prediction of protein binding sites in nucleic acids
- geneid - Gene prediction tool, it can also introduce homology and annotation evidences and produce a reannotation of a genomic sequence. A pthreads parallel version also available.
- LIBELLULA - LIBELLULA is a neural network based web server to evaluate fold recognition results
- UGENE - visual suite with integrated secondary structure prediction algorithms