All the commands in scanps_alias.dat are available for use on the command line. You can either specify the command or its alias, with or without a preceding - symbol. For example,
QSEQ_FILE hahu.seq -qseq_file hahu.seq -s hahu.seq
all do the same thing on the command line assuming the standard scanps_alias.dat file has not been modified.
A typical scan might be started by:
scanps -s hahu.seq -bdb swall -ugd 0 -ld_pen 8 -mode 0 > hahu.out
This would scan the sequence in file "hahu.seq" against the binary database called "swall" using a length dependent gap penalty of 8 with whatever default matrix file was specified in the scanps_defaults.dat file. The ugd 0 turns off the use of default gap penalty combinations stored in the file "scanps_gapdefs.dat".
More examples are given below.