Linkage disequilibrium

Joe Felsenstein joe at evolution.genetics.washington.edu
Fri Apr 10 07:10:26 EST 1998


In article <352C9492.182B at liverpool.ac.uk>,  <hnewbery at liverpool.ac.uk> 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  http://wbar.uta.edu  for a list of
available population genetics software.    Try GDA.  Also look into
some others not listed there:

POPGEN:      http://www.ualberta.ca/~fyeh/index.htm
POPGENE:     http://www.ualberta.ca/~fyeh/index.htm
GENEPOP:     http://anthropologie.unige.ch/arlequin/
and GENETIX: http://www.univ-montp2.fr/genome-pop/intro.htm

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

http://w3.ualg.pt/~rcastil/links.htm

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



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