SCANPS may be used in two ways, simple and advanced. To use the simple method, you only need SCANPS, a sequence query, a SCANPS defaults file and database file. To use the advanced features you ideally should have created indexes for the database file using the programs simclean and id_pir3. Please see the section 11 for details.
This manual assumes that the installation has been performed correctly, if you experience problems running the programs please see the section 11 and if that fails, send me an email!
Typing ``scanps'' on its own gives a list of the legal command line arguments. Most of these are described with examples in the following sections. They are also listed in Section 14.5.