Pub Quality Seq Comparison?

[Karen Peck-Miller]

I need to make a publication quality figure, showing an allignment 
between my cDNA sequence and other related genes -- one that draws 
boxes around the nucleotides that are different between the sequences, 
etc.  I have a Mac, and have been using MacDNAsis for everyday 
comparisons, but it doesn't seem to be able to do the publication 
quality job that I need.

Could anyone suggest DNA analysis software that could do this?  Thanks 
in advance.

Karen A. Peck-Miller, Ph.D.
National Marine Fisheries Service
Seattle, WA

Karen.A.Peck-Miller at noaa.gov