Meta-MEME standards

• Command lines follow the POSIX.2 standard, but always use long options preceded by a double hyphen. Required arguments do not have flags associated with them and occur at the end of the command line:

           command --flag1 option1 --flag2 required1 required2
        

• Programs are written in C or Perl. C programs reside in the src directory and are compiled into an architecture-specific subdirectory of bin. Perl programs reside in the bin directory.
• All programs provide a brief usage statement on the command line when they are typed with no arguments. Detailed documentation associated with program foo is given in doc/foo.html.