[EMBOSS] needle question!

[Karen Hayden]

Hello,
 I am currently using needle to generate an alignment between two
sequences which contain non-informative bases (ie, identified low
quality bases (phred scores) and have been changed to  "N").
Presently,  these bases are penalized as any other non-matching
character.  Is there any way to change needle to "overlook" these
bases when generating the best scoring alignment (or, do I need to
write my own version of needle?)

Thank you in advance for any advise you can offer!

Best regards,
Karen