I wish to analyze an alignment of two coding regions from a single gene.  When I upload the NEXUS file, specifying "Codon" as the data type, Datamonkey is telling me that it is finding stop codons all over the alignment (in every OTU).  However when I look at all three reading frames in Sequencher, it is clear that Frame 3 is devoid of stop codons, and I can see towards the end of the second exon sequence the characteristic amino acid sequence that earmarks this gene (WRKY).  I cannot for the life of me figure out why Datamonkey is mis-reading this file, unless it is because the 5' coding region is incomplete.  Could that be the problem?