Hello.
I've been scouring the website/forum for a few days now, while also dabbling with the program itself, but haven't gotten utility I need and was hoping someone could help.

I'm looking for something like Sequencher or Vector NTI that allows contig visualization of a forward and reverse output from 2 AB1 files. However, after contig I would like to edit any mismatches and trim primers/ends WHILE viewing 2 chromatograms stacked on each other. But I CANNOT use a reference sequence, as these are Unknown 16S region reads.

The closest I have gotten is using the CAP3, which automatically reverse/comp'd my reverse sequence... However, it doesn't look like the stacked chromatogram view that using a reference sequence appears.

Is there any feasible way of doing this properly, or has this not been implemented yet? 
Thanks! 
Josh