implement clustering/redundancy filter for peng output

[croth1]

This can be done with our model distance score. There is an older implementation of the score in my python implementation #5 - Since my implementation Johannes adapted the theory and now pads overhangs with background.

@AnjaSophieKiesel, do you have the lastest version of the scoring implementation somewhere available?

[AnjaSophieKiesel]

the scoring implementation is now in the /scripts folder -> "MMcompare_PMW.R"