Linkage disequilibrium

Joe Felsenstein joe at
Fri Apr 10 07:10:26 EST 1998

In article <352C9492.182B at>,  <hnewbery at> wrote:
> ... I am attempting to ascertain whether the two 
>polymorphisms are in linkage disequilibrium, based on the
>genotype frequencies in our study population.
>I have thus been trying to use the iterative method of 
>Hill to estimate P11, but it has not given me sensible answers.

It should.

>My query (rather long-winded, apologies)is thus whether 
>there are any programmes available (preferably, though 
>not necessarily) over the internet which will calculate the 
>degree of linkage disequilibrium between two polymorphisms for 
>me given the genotypes which we have encountered.

There are.  Try the web site  for a list of
available population genetics software.    Try GDA.  Also look into
some others not listed there:


I have drawn these from a nice web page by Rita Castilho at:

Joe Felsenstein         joe at
 Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA

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