I'd recommend Getopt::Long. It's easy to use, and easier to extend.

use Getopt::Long   qw( GetOptions );
use File::Basename qw( basename );

sub usage {
   my ($msg) = @_;
   print STDERR $msg if defined($msg);
   my $fn = basename($0);
   print STDERR "usage: $fn ...\n";    # XXX Fill in the "..."
   exit(1);
}

GetOptions(
   'a=s' => my $alignment_file,
   's=s' => my $scorecons_file,
   'i=s' => my $image_file,
   'm=s' => my $numbered_model,
   'c=s' => my $csa_file,
) or usage();

defined($alignment_file) or usage("Missing alignment file\n");
defined($scorecons_file) or usage("Missing score file\n");
defined($image_file    ) or usage("Missing image file\n");
defined($numbered_model) or usage("Missing numbered model file\n");
defined($csa_file      ) or usage("Missing CSA file\n");
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