Linkage analysis on inbred pedigrees

[Stephen L. Mathias]

Hello,
I am doing some linkage analysis (using FASTLINK) on an inbred dog pedigree
which contains several loops. I have broken these loops in the normal way by
duplicating individuals. However, it occurs to me that in doing this one loses
all the phase information from the duplicated individuals (because the
duplicated individual with offspring has no parents). This obviously seriously
reduces the power of my pedigree. Does anyone know a way around this problem?
Or are there better linkage analysis packages for use with inbred pedigrees?
-Steve
 
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                          Stephen L. Mathias
            Department of Genetics, University of Cambridge
                       Downing Street, Cambridge
                           England  CB2 3EH
Phone: +44 (0)1223 333986            E-MAIL: smathias at gen.cam.ac.uk
  Fax: +44 (0)1223 333992                    sm10016 at mole.bio.cam.ac.uk
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              Resist much. Obey little.    -Walt Whitman