Genotypic LD - Run Arlequin
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SNPator has an up to date version of the Arlequin software* installed in dedicated servers. The Run Arlequin option creates an Arlequin input file from data stored in SNPator. Then it runs Arlequin with this input file, calculating Genotypic Linkage Disequilibrium and sends the results to the User Results section.

In the Arlequin input file created in the process, data will be put grouped in a single sample or divided into different samples depending on the value you introduce in the box below:

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If you select a field here, the values of that field will be used as a categories to create different samples in the file.

Once the "Retrieve data" button is pressed, the process is launched. It can be followed in the Jobs section. Once it has finished, results will appear in the User results section. There will be a *.zip file containing:

- All the output files that Arlequin has generated during its execution

- arlequinProcess.log
It is a log of the messages that Arlequin shows during execution. It's what  users would see on their screen if they executed Arlequin on their workstation.

- Haploid data treatment.

* All genotypes are haploid

Arlequin runs with an Arlequin input file with one line per sample instead of the usual two in the diploid case.

* Some samples have diploid genotypes and other samples haploid genotypes.

Two different Arlequin input files are created for the diploid and haploid genotypes respectively. They are run separately.

* Haploid and diploid genotypes are mixed in the same samples.

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