I'm trying to do a multiple alignment of coding sequences for a protein I'm interested in, using Mega 5.05. Following the advice in Barry Hall's book, I'm trying to align the sequences using MUSCLE, aligning by codons. However, I keep getting an error during the alignment: "Stop codon(s) are found in the translated sequences. Please select a correct Genetic Code or coding frame." If I ignore the error and look at the translated protein sequences from the resulting alignment, I can't find any evidence of unidentified or termination codons within the sequences, just at the end (as I would expect). Am I misinterpreting the error, or if not, is there a way to figure out which sequence is causing the problem so I can decide what to do with it?