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Arlequin ver

(released on 02.08.2015)

About What's new Implemented methods Downloads Screenshots

Arlequin: An Integrated Software for Population Genetics Data Analysis


New R functions ar available (to work with R release 3.5 and above). Note that these new R functions are integrated into zip files for windows, mac and linux versions

Update of new version of arlequin ver, correcting a few bugs.


Update of new version of arlequin ver, correcting a bug in the computation of molecular diversity for DNA sequences (thanks to René Malenfant for reporting it).

Release of new version of arlequin ver 3.5.2.
It corrects minor bugs, adds computation of SFS from DNA/SNP data, and improves the reading and handling of long DNA sequences. More information on the new version can be found here.


Release of new R functions for R package ver 3.01 here. The zip file contains a directory called Rfunctions, which needs to replace the Rfunctions directory located in your Arlequin home directory.
If you have already installed Arlequin and update your R package to ver 3.01 (latest version in June 2013), then this update is necessary to be able to produce graphics in your xml files.


Release of maintenance version of arlequin ver, correcting minor bugs.

New versions of arlcore and arlsumstat ver for Mac OS X are available on the download page.

Kent Holsinger has kindly developed a MacOSX binary version of Winarl35 under WineBottler, which needs to be installed on your Mac.
More information and a downloadable version of WinArl35.dmg can be found here.

There was a minor bug in the first release of Arlequin version 3.5. Updated versions ( correcting this bug are now available on the download page.

Why is it called Arlequin?

Arlequin is the French translation of "Arlecchino", a famous character of the Italian "Commedia dell'Arte". As a character he has many aspects, but he has the ability to switch among them very easily according to its needs and to necessities. This polymorphic ability is symbolized by his colorful costume, from which the Arlequin icon was designed.

Arlequin phylosophy

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. 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.

Finally, we wanted Arlequin to be able to handle genetic data under many different forms, and to try to carry out the same types of analyses irrespective of the format of the data.

Because Arlequin has a rich set of features and many options, it means that the user has to spend some time in learning them. However, we hope that the learning curve will not be that steep.

Arlequin is made available free of charge, as long as we have enough local resources to support the development of the program.

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


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


  1. Choose which Text Editor to use when editing project files in the "Arlequin Configuration" tab.
  2. 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.


Unfortunately, the Genetics Software Forum has been locked due to spam attacks and lack of IT support.

The manual Arlequin35.pdf can be downloaded here.


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.

Last edit:  14.03.19 by Laurent Excoffier