Clinod requires Java 6 and the Batchman executable from the Stuttgart Neural Network Simulator [12] to run. Clinod accepts the list of FASTA formatted sequences from an input file and outputs the predictions to a file or the console. By default the following output is produced for each sequence-the name of the sequence, the number of NoLSs predicted, the start and the end positions and the sequences of each predicted NoLS. However, for better integration with other bioinformatics tools, many more output options are supported. For example, the input sequences can be cleaned (stripped of ambiguous characters), and output along with the prediction results and sequences with no predicted NoLS can be omitted from the output. Various output options are described in Table 1 but for a detailed description of the clinod switches please refer to Additional file 1.