I'd also suggest the IPC:: modules. For example, if you want to control the input and output of another program, try something like this (Perl Cookbook, pg. 567):

use IPC::Open2;

open2(*README, *WRITEME, $program)
print WRITEME "here's your input\n";
$output = <README>;
close(WRITEME);
close(README);
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If you want to control the input, output, and error use IPC::Open3.