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Have you tried it?
Read all of https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1002202, with special attention to rule #6.
Hello Helena!
Read and apply the manual (http://mummer.sourceforge.net/manual/)
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!