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Hi Mario,
I am happy to help with your GenomeBrowse questions.
The stand-alone version of GenomeBrowse is for visualization of data only, it does not have the functionality to estimate LD between markers.
Linkage Disequilibrium estimations are available in our SNP & Variant Suite (SVS) product. You can see an example of this analysis in our tutorial at the following link.
http://doc.goldenhelix.com/SVS/tutorials/ldhaplotypeanalysis/index.html
You can request access to SVS by filling out a request on our website at the following link.
http://goldenhelix.com/products/SNP_Variation/index.html
Let us know if you have any further questions.
Thanks, Jami...
Golden Helix Support