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 02.08.2015
Update of new version of arlequin ver 188.8.131.52, correcting a few bugs.
Update of new version of arlequin ver 184.108.40.206, 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.
Note that some programs can now be used to translate VCF files into arlequin project (*.arp) files like:
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 220.127.116.11, correcting minor bugs.
New versions of arlcore and arlsumstat ver 18.104.22.168 for Mac OS X are available on the download page. 11.10.2010 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 (22.214.171.124)
correcting this bug are now available on the download page.
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
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
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
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.
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
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
Arlequin35.zip to any temporary directory.
all files contained in Arlequin35.zip in the directory of your choice.
Arlequin by double-clicking on the file WinArl35.exe, which is the main
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
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.