(adapted from the original Genepop v3.1b documentation)
Only one test on contingency table is available to test for genotypic (for the diploid case) or gametic (for the haploid case) linkage disequilibrium. The null hypothesis Ho is: "Genotypes at one locus are independent from genotypes at the other locus". For a given pair of loci within one population, the relevant information is represented by GENEPOP by the following contingency table (here GOT2 and EST for the diploid Culex pipiens, presenting various genotype combinations):
GOT2
1.1 1.3 3.3 1.7 3.7
EST ______________________________
1.1 1 1 0 0 1 3
1.2 16 6 1 3 2 28
______________________________
17 7 1 3 3 31
GENEPOP creates all such contingency tables for all pairs of loci in each population, then performs a probability test (or Fisher exact test) for each table using a Markov chain (see OPTION 3 for details about this method).
For haploid data, use sub-option 3. GENEPOP will add the same imaginary allele (e.g. 01) in all individuals for all loci, and return this new data set via your web browser. Copy the data (or save it as a text file on your local machine) and paste it into the GENEPOP input text box after choosing sub-option 1 of OPTION 2: GENEPOP will build genotypic contingency tables for all pairs of loci in each population and test them. These tables correspond to a gametic association, because the same allele has been added to mimic a diploid genotype.
OUTPUT. Results are returned via the web browser (and/or you can also have the results emailed to you - this may be advisable for international users with large data files as the computations may take some time). Two intractable situations are indicated: empty tables ("Not possible"), and tables for which all rows or all columns marginal sums are 1 ("No information"). For each locus pair within each population, the unbiased estimate of the P-value is indicated, as well as the standard error. At this end, a global test (Fisher's method) for each pair of loci is performed across populations. All contingency tables (for n loci and p populations, there are p.n.(n-1)/2 tables) are available through sub-option 2. Tables will be returned to you via the web browser (and/or email).
Note. This option requires a memory space determined mainly by the number of individuals in the largest population, so that large number of loci (with up to 99 alleles per locus) and populations can be analyzed with this option. This is at the cost of some computing time during the process of constructing the contingency tables.
It is therefore recommended that you have your results returned by email only. Please report any problems or bugs that you encounter with the web version of this option to Eleanor Morgan