LD analysis using closely related species and distance is in Basepair

Question

[bioengine]

Hello all,

I am trying to do LD analysis to calculate LD decay/draw curve and calculate haplotype blocks. I have tried using HAPLOVIEW: which just gave me a big LD block. I am trying Plink, but my distance is in basepair, so when I draw graph, its just a square with all the SNPs scattered everywhere. I dont know how to proceed further. Can someone please help me in this regard.

Thanks