Apple's Java updates for Mac OS X 10.5 and 10.6 from October 2010 have caused the "Preferences" option in the "CodonCode Aligner" menu to disappear. All users of versions 3.0 to 3.7.1, and all users with a current update and support agreement, should update to version 3.7.1.1, which fixes this problem.
Users of older CodonCode Aligner versions who do not have a current update and support agreement can either