Linkage disequilibrium & Haplotypes

David MacHugh dmachugh at
Thu Mar 28 08:25:54 EST 1996


I have a query about using the GENEPOP program (Raymond & Rousset [1995]
J. Hered. 86(3): 248-49).

We have haplotypic data from a number of microsatellites typed in human
males on the X-chromosome. 
Basically we would like to determine the extent of linkage disequilibrium
among these markers (STRs) using the GENEPOP program.

Does anyone know of any theoretical objections to recoding the data as
pseudo-homozygotes and testing for LD?

Perhaps someone might know a more appropriate method for dealing with this
type of data.

Data format:

Individual 1: 120 145 130 210 151
Individual 2: 122 143 134 208 157


Thanks in advance,

David MacHugh,
Genetics Department,
Trinity College,
Dublin 2.
E-mail: dmachugh at

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