BOX.EXE takes the output from programs such as MACAW and draws boxes around the consensus amino acids as given by the alignment. The program takes ASCII files as input. Blocks to be aligned must be delimited by empty lines, eg. Sequence 1 ACDEFGHIKLMNPQRSTVWY Sequence 2 ACDEFGHIKLMNPQRSTVWY Sequence 1 YWVTSRQPNMLKIHGFEDCA Sequence 2 YWVTSRQPNMLKIHGFEDCA The user must specify the input filename, output filename and the number of the column from which BOX starts to draw boxes. The final parameter is to avoid the sequence names being boxed! Parameters can be entered from the command line in the following order BOX [infile] [outfile] [start col] The program prompts for any parameters that it cannot find on the command line. The line length can be up to 300 characters and up to 20 sequences can be boxed at one time. Problems / Suggestions: Ramin Nakisa, Biophysics Group, The Blackett Laboratory, Imperial College of Science, Technology & Medicine, Prince Consort Road, South Kensington, London SW7 2BZ. EMAIL: BIOPHYS@UK.AC.IC.PH.V1 USA : NSFNET-RELAY.AC.UK::BIOPHYS@UK.AC.IC.PH.V1 March 25, 1992.