1. Question related to stubbh01 or stubbh01f (stubb with motif correlations):
   Anti-correlated motif instances increase the free energy when correlation 
   parameters are included. I thought motif correlations only captures 
   scenarios where one motif consistently follows another. Is this an anomaly?

   Answer: This is expected. The way the positional correlations between 
   motifs are modelled, any kind of significant deviation from a random 
   positioning of the motifs (with respect to each other) will increase the 
   overall free energy score.

2. I ran the example commands for two species stubb, and the results dont 
   match with those in sample/test_output/two_species/.

   Answer: This could be because you are using a different version of lagan
   from the one that was used in creating test_output/two_species/ The output
   of different versions of LAGAN is known to be somewhat different.
