Can anyone recommend a user friendly free software to analyze alleles linkage disequilibrium?

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Christopher Delgado-Ratto

Fstat is useful for detecting pairwise LD.

http://www2.unil.ch/popgen/softwares/fstat.htm

For overall LD LIAN is a good option:

http://guanine.evolbio.mpg.de/cgi-bin/lian/lian.cgi.pl

Enjoy the discovering.

Salwa Hassan Teama

Allele linkage disequilibrium analysis software web..

http://www.genes.org.uk/software/LD-software.shtml

Travis G. Gerwing

In the past I have used Fstat, and Genepop as suggested by other respondents. I have also used Arlequin. Which program worked best depended on my data set! Enjoy!

Sang-Yong Eom

I want to recommend you a useful web tool for SNP analysis including LD estimation.

[SNPStats] http://bioinfo.iconcologia.net/SNPstats