the alleles library contains allele sequences for those only appear in the case and control samples
lib.names
the corresponding names of the alleles
case.sub
case subjects, two columns for two haplotypes
ctl.sub
control subjects, two columns for two haplotypes
aic.now
aic for the current model
dev.now
deviance for the current model
df.now
degree of freedom for the current model
rank
numbers of pairs with top similarity scores to be investigate
if FALSE, then deviance is calculated for the step-wise merger, then option "alpha" and "step" is used
cut
cutoff for similarity score to be consider, default is -1, means all scores above 0
delete.snp
a vector of position of deleted SNPs
ref
allele names for the reference level, the default reference level (ref="NA") is the most common allelels
alpha
family-wise error, used for deviance only
step
index for how many deletions have been carried so far
providing 
.