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First step: 
You need Python on your system to run DotKnot (http://www.python.org).

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Second step: 
Installation of the Vienna RNA package:

Switch to DotKnot_1.2/scr and type:
	tar -zxvf ViennaRNA-1.8.4.tar.gz
	cd ViennaRNA-1.8.4

The cutoff value for the base pair probabilities needs to be changed in the Vienna RNA Package.
In version 1.8.4, lines 258 and 263 of the Progs/RNAfold.c file need to change.
What currently reads:

pl1 = make_plist(length, 1e-5);
pl2 = stackProb(1e-5);

needs to change to 

pl1 = make_plist(length, 1e-11);
pl2 = stackProb(1e-11);

After changing the lines, type:	
	./configure
	make
and (as root)
	make install

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