Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-07-20T23:10:02.150Z
Answers.LastActivityDate: 2017-07-20T23:10:02.150Z
Answers.UserDisplayName: Remi.b
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-16T09:17:33.847Z
Answers.Text: Hi there, thanks for your contribution the link seems useful, but OP specifically asked for an example. It would be nice to provide one.
Answers.UserDisplayName: Kamil S Jaron
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-16T00:13:57.217Z
Answers.LastActivityDate: 2019-04-16T00:13:57.217Z
Answers.UserDisplayName: DLC
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-18T13:54:34.947Z
Comments.Text: 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: http://cmpg.unibe.ch/software/arlequin35/man/arlsumstat_readme.txt
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-18T13:58:15.603Z
Comments.Text: 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.
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-19T14:07:57.060Z
Comments.Text: 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"!
Comments.UserDisplayName: Remi.b
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-19T14:16:14.393Z
Comments.Text: I guess all these people had a windows version to start with. Searching for "Arlequin linux" got me the following page: https://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".
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-19T17:49:53.317Z
Comments.Text: @bli ok! I am surprised that Arlequin is not more user friendly. A reproducible example with Windows will still be helpful. Thank you
Comments.UserDisplayName: Remi.b
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-19T23:08:15.673Z
Comments.Text: Note that it may well be user friendly, for users that have windows. That's not the case of all bioinformaticians.
Comments.UserDisplayName: bli
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-20T23:19:19.817Z
Comments.Text: A follow-up question can be found [here](https://www.biostars.org/p/263837/) :)
Comments.UserDisplayName: Remi.b
Tags: <genome><r><positive-selection>
Title: How can I use Arlequin via the command line?
ThreadText: # How can I use Arlequin via the command line?
  
  (Asked by: username_0 on 2017-07-16)
  
  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.
  
  **Tags:** genome, r, positive-selection
  
  > **Comments:**
  > **username_1**: 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: http://cmpg.unibe.ch/software/arlequin35/man/arlsumstat_readme.txt  
  > **username_1**: 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.  
  > **username_0**: 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"!  
  > **username_1**: I guess all these people had a windows version to start with. Searching for "Arlequin linux" got me the following page: https://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".  
  > **username_0**: @username_1 ok! I am surprised that Arlequin is not more user friendly. A reproducible example with Windows will still be helpful. Thank you  
  > **username_1**: Note that it may well be user friendly, for users that have windows. That's not the case of all bioinformaticians.  
  > **username_0**: A follow-up question can be found [here](https://www.biostars.org/p/263837/) :)  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2017-07-20. Score: 3 | Accepted answer
  
  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).
  
  
  ---
  
  ### Answer by username_2 on 2019-04-16. Score: 1
  
  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>
  
  > **Comments:**
  > **username_3**: Hi there, thanks for your contribution the link seems useful, but OP specifically asked for an example. It would be nice to provide one.  
  
  ---
  
  