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CGI stands for 'Common Gateway Interface': it defines how scripts and executables should expect incoming data as well as how to send outgoing data to and from the client (normally the browser).
Perl is a programming language that is commonly used to write 'web apps'... but all web apps must 'speak' CGI if they are to work. For some languages, this is more 'automatic' than others (eg. PHP does a lot more grunt work than Perl, which does a lot more than C).
For some reason, people seem to thing that Perl is CGI and vice-versa, but they would be wrong.
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