Embedded stop codon in translated nucleotide sequences in DAMBE

Question

[Fathima]

I am using DAMBE to convert the alignment of nucleotide sequences to a PAML File, after trimming the terminal stop codon and the start codon (the sequence selected has no other embedded stop codon - as per shown in geneious alignment viewer). But, once the file is opened in DAMBE, it shows that the translated nucleotide sequence has an embedded stop codon. How do I solve this problem?

[Mensur Dlakic]

It is not obvious to me what exact steps you did here, but here is what I do know: there will always be stop codons even in open reading frames. If is fairly certain that you will have TAA, TAG or TGA in any long(ish) stretch of DNA sequence. As long as your stop codons are not in the main reading frame, it shouldn't matter. If as part of your procedure you have done any base trimming inside the coding region, these silent stop codons could be brought into a main frame like with any nonsense mutation.