Running WinArl on Mac OS X

Arlequin figure

Arlequin is a very flexible program for analysis of population genetic data. Unfortunately, binary executables are currently only available for Windows and Linux platforms, and the GUI is available only under Windows. If you're running Linux, you can probably figure out how to run the GUI using Wine without my help. If you're running OS X, the process is more involved. Here's what you do:

  1. Download a Windows setup version of WinArl (WinArl35-setup.exe). (Note to Windows users: If you'd rather run a setup program than unzip the files distributed on the Arlequin site, you can run this installer as you would any other. It won't ask you where you want it installed. It will just put it into "C:\Program Files\WinArl35" by default.)
  2. Install WineBottler. (Note to anyone using OS X v10.4. I've only tested this procedure on OS X v10.5 and v10.6, and I'm relatively new to Macs. My understanding is that X Windows was not installed by default in OS X v10.4 and earlier. You'll need to get X Windows installed before installing WineBottler.)
  3. Start WineBottler.
    1. Click on "Create Custom Prefixes" in the left column.
    2. Click on "select File" in the top right corner, navigate to where you saved WinArl35-setup.exe, and click on it. You should see the box fill with a long path ending with "WinArl35-setup.exe".
    3. Leave the "Copy only" box unchecked, and leave the "include Wine binaries" box unchecked. (Since you already have a copy of Wine installed on your computer -- otherwise you couldn't run WineBottler -- you don't need to include the binaries a second time.)
    4. Check the "Silent install" box, and click "Install". A dialog box will come up asking you to name the ouput file (I use "") and where to save it. Once you're satisfied you've got a name you can remember and you know where you are saving it, click "Save".
    5. WineBottler will churn for a little while, then you'll get a welcome to the WinArl3.5 Setup Wizard. Click "Next >", then click "Install", then click "Finish".
    6. When it asks you to "Select Startfile", accept the default ("Program Files/WinArl35/WinArl35.exe") and click "OK".
    7. You'll get a new message saying "Prefix created successfully." If you navigate to the folder where you asked to be saved, you should see it there. Click on it the way you would with any other Mac application and after awhile (it may take quite awhile if you've shut X Windows down), Arlequin will come up looking very much like it does on a Windows box.
  4. Alternatively, after you have WineBottler installed, you should be able to download WinArl35.dmg from here, install it the way you would any other Mac application, and run it to your heart's content. (I can't swear to this, because I haven't tried this approach, but I think it will work.)


I've encountered only two limitations with this approach.

  1. Arlequin won't launch a browser automatically to show you the results of your analysis. You have to navigate to the output directory, <basename>.res, and click on <basename>.htm yourself to see the results.
  2. Arlequin doesn't copy the Javascript necessary for <basename>_tree.htm to display the tree of results correctly in the left-hand frame, and it's necessary to edit the HTML by hand to get it to work properly once the Javascript is copied in.

Other than that everything seems to be just fine.


Laurent Excoffier, for making Arlequin available.

Aidan Findlater, for his instructions on using WineBottler to allow WinBUGS to run on Mac OS X.

Last updated: 26 September 2010, Kent Holsinger