Initializing variables to an empty string is generally no advantage. Why not collapse those declarations into one line?
my ( $help, $man, $version, $token_debug, $glossary_output, $dictionar
+y_output );
# or
my ( $help, $man, $version, $token_debug, $glossary_output, $dictionar
+y_output ) = ( '', '', '', '', '', '' );
GetOptions will also take a reference to a hash as its first argument, instead of all the variables. Much more concise and you don't have to worry three pages down what that variable was called.
--
TTTATCGGTCGTTATATAGATGTTTGCA
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