Input Alignment:	/home/users/fuchs/HelixCorrTest/example.fasta	#File containing sequence alignment
TMS File:		/home/users/fuchs/HelixCorrTest/example.tms     #File containing TMS positions
Result Folder:		/home/users/fuchs/HelixCorrTest/Results/	#Folder where result files should be stored
Required Correlations:	3						#threshold for required correlations:q per TMS pair
Use CAPS:		Y						#include CAPS prediction (Y) or not (N)
CAPS Output File:	/home/users/fuchs/HelixCorrTest/caps.out	#File with CAPS output (only valid in case CAPS prediction is included)
Use CorrMut:		Y						#include CorrMut prediction (Y) or not (N)
CorrMut Output Folder:	/home/users/fuchs/HelixCorrTest/		#Folder with complete CorrMut output (only valid in case CorrMut prediction is included)