Hi. I can recommend you mauve:

http://darlinglab.org/mauve/mauve.html

Best regards,

---sram

yes mauve is popular one but i need the software that takes already annotated genome data in fasta file

Please consider that a fasta file does not include general/proper/standard annotations.

A fasta file is only a name and sequence. Some people encode annotations in the name in non-standard way sometimes, but as such, programs cannot rely on them. Normally a fasta file can be accompanied by GFF file that annotates somehow a fasta file. But this is an external file. 

Genbank files for example includes both the sequences and the annotations, on the other hand. 

I am not sure about what you are looking for. Can you provide a link or an image of an example of what you want to do? for example if you have seen what you want in some published article that we can see?

Best regards,

---sram