I have a SNP data set to test for Linkage disequilibrium across all loci and I am running the command line in Genepop. I cannot use Plink to test for LD as my SNPs are not mapped (they were generated via a de novo approach). According to my calculations, the job would almost 3000 days to complete... (obviously not ideal). Is there a way I can calculate linkage disequilibrium on a large data set of SNPs? is there a way to speed up the process?