Arlequin Introduction

The goal of Arlequin is to 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 analyses they want to perform on their data.
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.
Arlequin is made available free of charge.

Implemented methods

The analyses Arlequin can perform on the data fall into two main categories: intra-population and inter-population methods. In the first category statistical information is extracted independently from each population, whereas in the second category, samples are compared to each other.

System requirements

Windows 95/98/NT/2000/XP/7/8 (probably 10) A minimum of 512 MB RAM, and more to avoid swapping At least 30Mb free hard disk space

Installation

Download Arlequin35.zip to any temporary directory.
Extract all files contained in Arlequin35.zip in the directory of your choice.
Start Arlequin by double-clicking on the file WinArl35.exe, which is the main executable file.

Configuration

Choose which Text Editor to use when editing project files in the "Arlequin Configuration" tab.
Locate the Rcmd.exe program to embed graphs in your result project (needs the R statistical package to be installed)
The first thing to do before running Arlequin for the first time is certainly to read the manual. it will provide you with most of the information you are looking for. So, take some time to read it before you seriously start analyzing your data.
The manual Arlequin35.pdf can be downloaded here.

Citation

Please make sure that you are citing the right reference if you are using version 3.5.x of Arlequin:
Excoffier, L. and H.E. L. Lischer (2010) Arlequin suite ver 3.5: A new series of programs to perform population genetics analyses under Linux and Windows. Molecular Ecology Resources. 10: 564-567.