you can short your sub a lot:

sub get_Hx{
  my $site = $_[0];
  my $no_of_sequences =length($site);
  my $sum = 0;
  foreach(qw/A C D E F G H I J K L M N P Q R S T V W Y _ \./){
    my $count = () = $site =~ /$_/g;
    $sum += -($count/$no_of_sequences)*log_2($count/$no_of_sequences) 
+if($count > 0);
  }
  return $sum;
}
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