From University of Bern:
Arlequin provide the average user in population genetics with quite a large set of basic methods and statistical tests, in order to extract information on genetic and demographic features of a collection of population samples. The graphical interface is designed to allow users to rapidly select the different analysis they want to perform on their data. We felt important to be able to explore the data, to analyze several times the same data set from different perspectives, with different selected options. The statistical tests implemented in Arlequin have been chosen such as to minimize hidden assumptions and to be as powerful as possible. Thus, they often take the form of either permutation tests or exact tests, with some exceptions. Because Arlequin has a rich set of features and many options, it means that the user has to spend some time in learning them.