title: Conflict between MAFFT and new PRANK installation
body: <p>I had <a href="https://mafft.cbrc.jp/alignment/software/" rel="nofollow noreferrer">MAFFT</a> running fine on my computer (MacOS 11.6), until I downloaded <a href="http://wasabiapp.org/software/prank/" rel="nofollow noreferrer">PRANK</a> (a probabilistic multiple alignment program distributed by Wasabi) which also runs on its own MAFFT Unix executable file. The original MAFFT is located in the directory /usr/local/bin, and PRANK and its associated files live in another directory called /programs/prank/bin, both of which are in my $PATH variable, with the /usr/local/bin directory having priority. Now, not only is the MAFFT within PRANK giving the error below when I type the ‘prank’ command, but I also get this error when trying to use my original version of MAFFT by typing ‘mafft.’ Deleting my original MAFFT and only using the PRANK version does not fix things. If I fully delete PRANK and MAFFT and redownload MAFFT alone, I can get it to work again.</p>
  <p>I’ve tried all the steps listed in the error output below. My $MAFFT_BINARIES file appears to be empty or nonexistent, and there is no MAFFT_BINARIES line in my .bash_profile or any of the other settings files listed.</p>
  <p>Does anyone have any insight into what may be causing this or how I should go about fixing it? Has anyone experienced the same conflicts with PRANK? Please let me know if I can provide any additional information about my system or set-up that would be helpful. As you might be able to guess, I'm not particularly experienced in this level of digging around in the guts of my file directories, but I know just enough to get myself into trouble...</p>
  <pre><code>Error: Initial alignment with Mafft failed. The output generated was:
  
  v7.490 != v7.450 (2019/Aug/23)
  
  There is a problem in the configuration of your shell.
  Check the MAFFT_BINARIES environmental variable by
  $ echo $MAFFT_BINARIES
  
  This variable must be *unset*, unless you have installed MAFFT
  with a special configuration.  To unset this variable, type
  $ unset MAFFT_BINARIES
  or
  % unsetenv MAFFT_BINARIES
  Then retry
  $ mafft input &gt; output
  
  To keep this change permanently, edit setting files
  (.bash_profile, .profile, .cshrc, etc) in your home directory
  to delete the MAFFT_BINARIES line.
  On MacOSX, also edit or remove the .MacOSX/environment.plist file
  and then re-login (MacOSX 10.6) or reboot (MacOSX 10.7).
  
  Please send a problem report to katoh@ifrec.osaka-u.ac.jp,
  if this problem remains.
  </code></pre>