Software for comparative genomics of prokaryotes
 

Dear people,

can somebody suggest some software tool for comparative genomics of bacteria? It would be great to have a standalone software that is not web-based. I'm looking for a tool that is able draw synteny plots, can take the annotation of a reference genome and apply it to the new assembled sequence.
Additional it would be great to have a software that can connect the synteny with the sequence (like the Synmap and Gevo).

Maybe some can help!

Many thanks in advance!

Best regards,
p

What software are you using, if any?
 

I am looking for the different options that there are for doing the sames tasks that you mentioned in your question. Could you or anyone help me improving the list that I have so far?

MUMmer http://mummer.sourceforge.net/
CoGe http://genomevolution.org/CoGe/index.pl
Vista tools http://genome.lbl.gov/vista/index.shtml