title: Launching ClustalX2 and a file in it from java
body: <p>I have successfully launch <code>clustalx</code> from java(using only <code>/home/b/Desktop/clustalx-2.1-linux-i686-libcppstatic/clustalx</code>) but cannot launch a file in it directly.
   Here are the <code>code</code>  what i have tried:</p>
  
  <pre><code> String[] command= {"/home/b/Desktop/clustalx-2.1-linux-i686-libcppstatic/clustalx", "/home/b/Desktop/clustalx-2.1-linux-i686-libcppstatic/"+ "infile=F1F2CXAT211-alignment.aln" +".input"};
   String outlist[] = runCommand(command);
  </code></pre>
  
  <p>It is Running successfully without displaying clustalx.</p>