##Do you want to estimate the haplotype frequencies only or also test the association
##(1 only haplotype frequency; 2 both estimate haplotype frequency and test association)
2
##The input data file and output file names (include the path if not in the current directory;less than 100 charactors) 
input.txt   output.txt
##If only affected children (qualitative trait) were considered, write 1 in next line; otherwise, write 0
0
##How many markers considered
5
##The location of each markers (in kb) separated by blank space 
0  100 200 300 400 
##Number of alleles in each of the markers
2 2 2 2 2 
##Number of permutation used to evaluate the p-value of the test
1000
##How many individuals in the data set?
13
##How many markers in each partition?(we suggest <=30 markers in each partition; 
##if there are many missing values <=15; if there are many families without parents <=6)
5 
##Do you want to marge the rare haplotype (0 no marging; 1 merge)
0
##If marging rare haplotype, give the cutoff of the rare haplotype frequency
0.01