First of all, be sure that you (=user under which php runs) are allowed to call the external program (OS access rights, safe_mode setting in php.ini). Then you have quite a few options in PHP to call programs via command line. The most common I use are:
system
This function returns false if the command failed or the last line of the returned output.
$lastLine = system('...');
shell_exec or backtick operators
This function/operator return the whole output of the command as a string.
$output = shell_exec('...'); // or:
$output = `...`;
exec
This function returns the last line of the output of the command. But you can give it a second argument that then contains all lines from the command output.
$lastLine = exec('...'); // or capturing all lines from output:
$lastLine = exec('...', $allLines);
Here is the overview of all functions for these usecases: http://de.php.net/manual/en/ref.exec.php