I need to compare aligned genomes and visualize it with dotplot. I have used Gepard and D-Genies but I don't see the possibility to add clusters IDs into the chart. Also, cause of the large alignment file it is almost impossible to add this information by myself in graphic program. I was looking for some kind of solution in R? Is there a package where I can do similar plots to those generated by Gepard?
Many thanks for any suggestions,