Downstream analysis of plink.blocks.det?

[Nikos]

I've managed to generate a plink.blocks.det file for an oat genome, with blocks that look pretty good visually. Now I'm interested in downstream analyses, in particular grouping individuals based on their haplotypes, in particular for some of the larger blocks.

The issue: some of my blocks span >1000 markers. As can be expected, no two individuals have identical sequences for the block as a whole. It is clear that there are a few major groups for these blocks, and I've considered eg using some standard clustering methods to split based on that, but I imagine I'm not the first person to be in this situation. Is there a best-practice way of grouping individuals in this situation? E.g. haploview produces matrices of haplotype sequences, but it also doesn't produce blocks of this size(?). Does plink offer some similar tool?

All the best,

Nikos Tsardakas Renhuldt