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For other uses, see Harlequin (disambiguation).

Arlequin is a free population genetics software. It performs several types of tests and calculations, including Fst, computing genetic distance, Hardy-Weinberg equilibrium, linkage disequilibrium, mismatch distribution, and pairwise difference tests.

It is currently in version 3.5 and is only available for Windows, though the previous version is still available for Windows, Mac OS X PPC, and Linux.

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