Usually, the programmer includes a "-h" option for displaying the synopsis, or simply lets Getopt::Long throw an error when "-h" or "-?" is used as an option, and makes sure to display the synopsis whenever Getopt::Long throws an error.

What would the synopsis be for your script? Why would you need a subroutine to process your options? What do "$substr1" and "$substr2" contain (where is the code that assigns values to those variables)?

In addition to what has been said, you could make the array variable "aminos" global, so that it can be accessed by all. But it's better to make a variable available close to where it's are needed.

Your values to your scalar variables maybe gotten from the CLI and checked if initialized.

Modifying your post a bit like this works, but you might still have to work on it or incorporate it with your code.

use warnings;
use strict;
use Getopt::Long qw(:config gnu_getopt);

help() if $ARGV[0] !~ /^--/;

my @aminos = qw (A R N D C Q E G H I L K M F P S T W Y V B Z X);

GetOptions(
    'substr1=s' => \my $substr1,
    'substr2=s' => \my $substr2,
    'sub'       => \&a,
    'help|?'    => \&help,
);

sub a {

    if ( "$substr1$substr2" =~ /[^@aminos]/ ) {
        print "hello\n";
    }

    print "@aminos\n";
}

sub help { print "Usage: script --substr1 value --substr2 value --sub"
+; exit }
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Note, I didn't check for the initialization of substr1 and 2

and please you don't need to always start a new thread!

yes .. sorry for that... and thank you very much for your answer :)