Hi,
you can use the
ACT software from the sanger institut (
http://www.sanger.ac.uk/resources/so...act/#downloads). It is free and you can download really easily on your computer. For me, the application is better in your computer, because you can work when there is no internet, as in the bus!!
Also, if you want to make beautiful figures of your genomic comparisons, you can use
Easyfig (
http://easyfig.sourceforge.net/).
I don't know if that answer to your question,
So good luck