Data retrieval: Formats - Arlequin
Previous  Next

This section generates a properly formatted and ready-to-use file that you can use as an input file for the Arlequin software*:

The resulting file is formatted to perform linkage disequilibrium tests in Arlequin.

Once this option is executed, a *.zip file appears in the User results section containing:

- information.txt
SNPator related information to identify the job: date, time, user, study and filter.

- arlequinConfigFile.inp
     The input file for Arlequin

This file will contain two comment lines at the top indicating what SNPs have been used and what SNPs have been discarded in the creation of the file.

Moreover, the data will be put together in only one sample or divided into different samples depending on the value of the box Group By:

graphic

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


- Haploid data treatment.

When haploid data are used in this section, three scenarios are possible:

* If all genotypes are haploid

An Arlequin input file is generated with one line per sample instead of the two in the diploid case.

* If some samples have diploid genotypes while other samples have haploid genotypes.

Two different Arlequin input files are created for diploid and haploid genotypes, respectively.

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

An error message appears and no action is taken.
     
References: