Estimating effective population size (Ne) using ~1 million SNPs

Question

[Abdel]

Is there a tool/software package that can compute Effective Population Size (Ne) based on LD in ~200 individuals with ~1 million SNPs? I spent some time trying NeEstimator v2 (http://molecularfisherieslaboratory.com.au/neestimator-soft ), but it turned out this tool does not handle too many genetic variants very well...

Many thanks in advance!

Answer 1

[akang]

Although its too late to reply but you might find your answer on How Can I Estimate Effective Population Size From Linkage Disequlibirum (R^2) Result?