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Scott, Nitin and Ross
Scott pointed out that Weir's composite LD is essentially a pearson correlation between 2 loci coded as 0,1,2 for the count of an arbitrary allele R will happily estimate pearson correlation matrices but for 5000 SNP, the amount of RAM needed is prohibitive. Some googling later, we found http://code.google.com/soc/gnu/appinfo.html?csaid=7211BC2F22A5A01E which holds promise, offering an R dataframe which can page itself out to a sqlite database (!).
Ross will get an alpha tarball built next week - Weiliang has been out on paternity leave - twin boys arrived a little over 2 weeks ago (congratulations!) and they have been keeping Weiliang busy (and Mrs Qiu even busier probably!).