Simplify reads the file simplify.txt to find the equivalences you desire. The first letter in each equivalence row is the letter that is substituted for all of the rest of the letters in the row. The simplify.txt file in the public data directory is only appropriate for simplifying peptide sequences. You must create your own simplify.txt file to define equivalences for nucleic acid simplifications. The parameters and switches listed below can be set from the command line.
List writes a list file with the names of the output sequence files.
If you don't specify a filename, then Simplify makes one up using Simplify for the filename and .List for the filename extension. This program normally monitors its progress on your screen. However, when you use the -Default option to suppress all program interaction, you also suppress the monitor. You can turn it back on with this option. If your program is running in batch, the monitor will appear in the log file.