If you use the consensus align feature rather than extracting the consensus sequences yourself then there will be links back to the contigs. Just select the contigs you want to align, click the alignment button and choose consensus alignment. Make sure you set the consensus options as you prefer since Geneious doesn't know what consensus settings you used for each document so you need to decide at this point otherwise the consensus can be truncated (just copy the settings from one of your contigs and you should be fine). You will then get an alignment of the consensus sequences and links back to the original contigs.

Shane

Thanks for the reply. However, what I mean (and I think this is what PollyA also wants in another recent post) is that I would like to do a multiple alignment of contigs where the consensus sequence from the contig is the "default view" (as you get from "Create an alignment of consensus sequences only"), but where you have the option to view the individual traces from each contig in the same window (e.g., above the consensus sequence. I think that CodonCode aligner has this option.

What we will probably do in future versions (although not in time for the upcoming 5.1 release) is to provide a little +/- button to the left of each of the consensus sequences in your alignment to make it expand out and show all the reads that contributed to that consensus sequence inline in the alignment directly beneath their consensus sequence. Is that the sort of user interface you'd expect to see?

Yes, that would be great. It would also be nice if the consensus alignment option was available for added files only, i.e., say I have an alignment of text-sequences and/or contig consensus sequences, and like to add a contig consensus.

Thanks

Adding a contig to an existing alignment so that it works with the proposed +/- buttons sounds useful. We will probably implement that too at the same time.