+ The way that you launch Jalview from the command line depends on the
+ platform you are on, and how it has been installed.
+
+ <ul>
+ <li>Standard installation on Linux/Unix:<pre>
+ /PATH_TO_JALVIEW/Jalview -open http://www.jalview.org/examples/jpred_msa.fasta -annotations http://www.jalview.org/examples/jpred_msa.seq.concise -colour Clustal</pre>
+ </li>
+ <li>Standard installation on Windows:<pre>
+ \PATH_TO_JALVIEW\Jalview.exe -open %HOMEPATH%\myalignment.fa</pre>
+ </li>
+ <li>OSX Application:<pre>
+open /Applications/Jalview.app --args -open ~/myalignment.fa</pre><em>(put
+ all the Jalview arguments <em>after</em> the --args parameter)
+ </em><br />
+ <br /></li>
+ <li>Jalview standalone executable Jar<pre>
+ <Path to Java home>/bin/java -jar %lt;Path to Jalview Jar>/jalview-all-1.8.jar -open myalignment.fa</pre></li>
+ </ul>