Display Open Reading Frame on Clustal alignment

Question

[andynkili]

I would like to compare different strains of a viral genome. Especially when it comes to.
I do a multiple alignment (clutalw) and look for SNPs that occur in CDS. Therefore i would like to display Open Reading Frame directly on the aligned sequences. I know that some alignment visualization tools like UGENE do display ORFs, but only on sequences individually not directly on the alignment.
Are there other tools that i'm not aware of, which might accomplish that or should i make my own orf finder that parses ".aln" files and outputs only ORFs that contain SNPs?

[abascalfederico]

This may help: with Jalview you can translate DNA alignments to amino acid alignments. The two windows communicate between them, so you can see which bases correspond to which amino acids. Jalview translates assuming reading frame is +1. If you want to modify this you could remove the first or the two first bases of the alignments (to get +2 and +3 reading frames, respectively).