Hello,

I have multiple sequence alignment files, some of NT some of AA. I wanted to plot similarity of these alignments along the coordinates of the alignment.

Basically the alignment should highlight regions that are very conserved among sequences and regions that are very divergent.

Something similar has been achieved here:

http://www.biology.wustl.edu/gcg/figure/plotsimilarity_1.gif

I am having no luck finding this in google.

Thanks, Adrian