Dear all

I have studied Linkage Disequilibrium on genotyped data (SNP chip) from 6 month ago. I read in many article that they did haplotype Reconstruction by several algorithm, such as Parsimony methods: Clark’s algorithm, Likelihood methods: E-M algorithm, Bayesian methods: PHASE algorithm. as I am new in this kind of analysis, i was confusing that the where do the result of haplotype reconstruction was used in LD analysis?

it use in calculation of r2 and D' or in Phase persistence ? or it calculated just for count haplotype frequency in population?

in Phasing process we calculate a correlation or regression between same SNP pair r2 in each distance for two population Because in different populations or breeds a pair of SNP may have the same value of r2 but different LD phases (Goddard et al., 2006). i have 5 different population of cattle and when i calculated the r between two breeds the amount of r was too low . when i check the amount of r2 as random in two population they had considerable different. and now, i dont know why?

is there any one that explain for me where and how we used the haplotype reconstruction result in LD analysis?