I'm trying to do a very simple thing: align 5 genes (exons + introns). Currently what I do is: align them with stretcher (EMBL-EBI) -> visualize with Jalview -> annotate exons and introns by hand.

My problem is that this is highly inefficient and I tend to mess up somewhere. Also, I need to re-annotate them every time I re-generate the alignment as a result of parameter tuning.

I was wondering if there is an alignment/visualization tool that can take into account the annotation information that can be supplied as, for example, a bed file. And "lift over" the annotation in the bed file to the alignment during visualization.

Thank you so much~