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 _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
