Pls cite "Shi YY, He L. SHEsis, a powerful software platform for analyses of linkage disequilibrium, haplotype construction, and genetic association at polymorphism loci. Cell Res. 2005 Feb;15(2):97-8." if you used this platform for research study, thks.

Given you use the haplotype analysis function, pls cite "Li Z, Zhang Z, He Z, Tang W, Li T, Zeng Z, He L, Shi Y. A partition-ligation-combination-subdivision EM algorithm for haplotype inference with multiallelic markers: update of the SHEsis ( Cell Res. 2009 Apr;19(4):519-23." too, thks.

Any question, pls contact YongYong Shi. Here is a simple introduction (Chinese Version).

Choose the analysis you need :
Single site analysis
Pair-loci D'/r2 value
Haplotype analysis
Number of sites :
Selected sites for haplotype analysis:
e.g. "1 1 0 1" to choose 1st, 2nd & 4th sites for hap-analysis when there is 4 sites in total. Error input will be recognized as default -- "1 1 1 1 ..." (all chosen).
Calculate linkage disequilibrium in:
You can compare linkage disequilibrium in different groups.
Lowest frequency threshold (LFT) for haplotype analysis:
Default value is 0.03, any number in [0, 1) could be accepted. Haplotype with frequency less than this number will not be considered in analysis.
Marker names (please use space to split variation names) :
Input data of control

Caution: The format of input data should be --

ID1 G A 1 1 a b ...

ID2 A G 1 2 b b ...

ID3 G G 1 1 c c ...


Here, the first column refers to the sample ID;

the second & third column refer to the alleles of the 1st site;

fourth & fifth for the 2nd site;

sixth & seventh for the 3rd site;


Pls use "0" for the missing alleles.

Input data of case