How can I use Arlequin via the command line?

I've got a decent knowledge of programming (incl. bash scripting) but I fail to understand how Arlequin works. Could you please help me with a very simple reproducible example on how to use Arlequin via the command line?

As the .zip file comes with its pre-compiled version, I'll just note that I'm on Mac OS X but of course, a reproducible example with Linux (or at worst with Windows) would also be helpful.

• In the manual, I read in the "systems requirement": "Windows XP/Vista/7". I guess that what you want to use is the arlumstat thing described here: cmpg.unibe.ch/software/arlequin35/man/arlsumstat_readme.txt
– bli
Jul 18 '17 at 13:54
• But in this readme file, it says you need a configuration file generated by the windows version of arlequin. This software looks rather messy. If you know the formulas to compute your statistics, you might in the long run benefit from implementing the calculations by yourself or find a bioinformatician friendly alternative package.
– bli
Jul 18 '17 at 13:58
• I don't know if Arlequin is messy but the version 3.5 alone has been cited 15274 times! I sure could implement the technic myself but I specifically want to use some commonly used software. I don't think there exist other implementations of FDist since Lositan "disappeared"! Jul 19 '17 at 14:07
• I guess all these people had a windows version to start with. Searching for "Arlequin linux" got me the following page: trapa.cz/en/arlequin-r-linux This person confirms that he had to run the windows version first. He did it using wine, a kind of windows emulator for linux. I don't know what the options are for MacOSX. I will definitely not call this program "bioinformatician-friendly".
– bli
Jul 19 '17 at 14:16
• A follow-up question can be found here :) Jul 20 '17 at 23:19

For MAC OSX, the executable found in arlsumstat_macosx (arlsumstatmac_64bit) seem to work appropriately. The directory for arlsumstat_macosx does not contain any examples but you can use example files from arlecore_macosx/Example files_linux using this syntax.

The complication is that arlsumstatmac_64bit will look in the current directory for the file arl_run.ars. There is a file with the same name in arlecore_macosx but it is not compatible. So you have to be in the arlsumstat_macosx.

In short, cd to arlsumstat_macosx and do

./arlsumstatmac_64bit path/to/arlecore_macosx/Example\ files_linux/Freqncy/cohen.ars path/to/arlecore_macosx/Example\ files_linux/Freqncy/cohen.arp


, where the .arp file contains the data and the .ars file contains the settings (the description of what you want Arlequin to do).

A concise description for using Arlecore on terminal for MAC, LINUX or Windows is provided here: http://cmpg.unibe.ch/software/arlequin35/man/arlecore_readme.txt

• Hi there, thanks for your contribution the link seems useful, but OP specifically asked for an example. It would be nice to provide one. Apr 16 '19 at 9:17