A quick mummer run

Suppose we want to perform a comparison of two closely related genomes:

  • Mycoplasma genitalium
  • Mycoplasma pneumoniae


    Ever wonder what a mummer is? See link.

    Launching mummer

    On the command line...
      % mummer GMG.1con GMP.1con > myco.out

    Launching mummerplot 

     % mummerplot myco.out
    And then view the results... 
     % gnuplot out.gp

    Not very interesting, try it on the protein level. 

      % promer GMG.1con GMP.1con > myco.out
    The resulting file is called out.cluster. Create a gnuplot file for that... 
      % mummerplot out.cluster
    And then view the results... 
     % gnuplot out.gp
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