Alignment & visualisation of two similar contigs

[TabeaK]

Hi guys!

I am currently trying to figure out how to compare two or more similar contigs on a global scale. I have my reference contig and a selection of corresponding contigs from other strains. Contig size is between 500.000 and 2.000.000 bp.

Is there a useful tool to do & visualize this?

I have come across MUMmer and will look into that, but how to visualize the output - preferably in a manner that I can scroll through the alignment - is completely unclear to me right now.

[GenoMax]

Give Mauve a try: http://gel.ahabs.wisc.edu/mauve/

[TabeaK]

Cheers, I'll play around with this a little!