text: user888: 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.
  
  user4438: 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
  
  user888: 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).
  
original_text: 888: <p>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?</p>
  
  <p>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.</p>
   4438: <p>A concise description for using Arlecore on terminal for MAC, LINUX or Windows is provided here:
  <a href="http://cmpg.unibe.ch/software/arlequin35/man/arlecore_readme.txt" rel="nofollow noreferrer">http://cmpg.unibe.ch/software/arlequin35/man/arlecore_readme.txt</a></p>
   888: <p>For MAC OSX, the executable found in <code>arlsumstat_macosx</code> (<code>arlsumstatmac_64bit</code>) seem to work appropriately. The directory for <code>arlsumstat_macosx</code> does not contain any examples but you can use example files from <code>arlecore_macosx/Example files_linux</code> using this syntax.</p>
  
  <p>The complication is that <code>arlsumstatmac_64bit</code> will look in the current directory for the file <code>arl_run.ars</code>. There is a file with the same name in <code>arlecore_macosx</code> but it is not compatible. So you have to be in the <code>arlsumstat_macosx</code>.</p>
  
  <p>In short, <code>cd</code> to <code>arlsumstat_macosx</code> and do</p>
  
  <pre><code>./arlsumstatmac_64bit path/to/arlecore_macosx/Example\ files_linux/Freqncy/cohen.ars path/to/arlecore_macosx/Example\ files_linux/Freqncy/cohen.arp
  </code></pre>
  
  <p>, where the <code>.arp</code> file contains the data and the <code>.ars</code> file contains the settings (the description of what you want Arlequin to do).</p>
  