I want to align two sequences in MUMmer. Is ./mummer -mum 1.fasta 2.fasta the way to go ?
./mummer -mum 1.fasta 2.fasta
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.
Read and apply the manual (http://mummer.sourceforge.net/manual/)
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