Hi Yann.
Jan suggested the VARNA pairwise alignment demo might be useful for a couple of situations in his project. (see my last jalview development list email today - specifically use case 4 - comparing two rna secondary structures and use case 5 : editing a newly copied structure in context of some consensus).
I was just wondering - is there any documentation for the alignment plot, so we can learn exactly what it is showing ? I kind of get the idea from the example, but I'm not sure exactly what the colours actually mean.
Jim.