I'm trying to align 15 genbank files generated by RAST for 15 Mycoplasma genomes that we have assembled. I am aligning the files with progressivemauve with default parameters, and visualizing with MAUVE's GUI. The alignment runs fine, but when I visualize it, I get "(no annotations loaded)" for each genome. I've tried this using a genbank file for a reference Mycoplasma genome and I get the same result.
Has anyone run into the problem before and/or does anyone have any suggestions?