Dear Meelad

Haploview would be the most user-friendly way to perform haplotype analysis.  Are you working with human DNA? If so you should only have 'two letters' representative of a diploid species. If not you may have more and haploview will not prove useful. If you are familiar with R then you can use Haplostats to perform your analysis.

Good luck!

Dear  Nathaniel 

Thanks for reply, but what I meant is that sometimes the blocks of my genotypes being of two letters and other times with three letters ..and I recently found this is associated with HaploView settings

but please there is something else I want to know ..

how to make association step between case and control in HaploView program ?

Dear Meelad

I'm not sure I'm fully following what you mean?  Do you mean a pairwise vs tri-allelic haplotype blocks? That is, three SNPs in a haplotype block inferring significance?  Perhaps if you attach your Haploview output files I could be of more assistance.

Dear  Nathaniel

thanks for interest,

well .. yeah I meant pairwise blocks and triple allele block but I discovered that the setting can be manipulated by user especially for D prime  from the Customized Block option..

but now i'm asking about the case/control association test of HaploView program and the estimation of haplotype frequency ..actually I see it inconclusive and I do not know how to interpret the results!!!

Best regards