Hi: I need to use Mummer for the alignment of two strainds of the complete genomes from Aspergillusfumigatus a239 and fgsca3, when I got the mummerplot the results seems scattered, I suppose that for this two type of genomes as being almost similar I should get almost a perfect diagonal in mummerplot? does anybody knows what parameters should I use in mummer for this type of alignments? also which option of mummer will be more exact? Thanks
You probably used nucmer for the alignment? If you try using promer (takes a significant longer time) it will usually elininate most of the noise/scatter (asmentioned coming from duplications/repeats and such). Result in most of our cases a more cleaner but highly similar plot (but on protein so its a different method/answer actually).