Command line control is described in detail in the Command Line Control section of the User's Guide . Information under this topic heading states where the ideas and the code for each program came from. If there are publications on which the program is based, they usually appear here unless they have not been mentioned under previous topic headings. If the program came from GCG but code did not originate at GCG, we try to cite the original code's author here. If you feel your work has not been acknowledged correctly, please complain.
Some programs require nonsequence data.
For instance, the mapping programs require the file enzyme.dat, which associates restriction enzyme names with their corresponding recognition sites. Normally these files are read from the public data directory and you need not provide them or even know about them. But if, for any reason, you wish to use your own data, you can use the Fetch program to copy the public version and use an editor to modify it to suit your needs. Programs read your version of a data file in preference to the public one. If the data file is not specified on the command line, the program checks your current directory.