I was wondering if there are any modern tools for visualization of whole-genome alignment, with ability to add annotation, and maybe extract variants? I've tried Mauve and Harvest so far, but they seem pretty abandoned and work quite poorly.
Are there any modern projects you can recommend? Surely with more and more genomes becoming available, there should be some tools to compare them? I am looking for something tailored to bacterial comparison, ideally, but any leads are welcome.