text: user16811: I want to manually fold and pair two sequences (U4 and U6). And I want to make niceish figures.
  I haven't found a single program that does that.
  thanks
  
  user3848: The RNA viewer that is particularly good is VA RNA. This stands for "Visualisation Applet for RNA". Its a java app and run it via,
  java -jar /Route2Progam/vaRNA/VARNAv3-93-API.jar
  
  Where Route2Progam is the path to where the jar files is stored, all other info in the run code is literal.
  Very nice pictures, point and clicky, drag structures into different shapes and easy to colour ... so for a GUI its great.
  They recommend PsuedoViewer for psuedoknots, but if that doesn't mean much ... it doesn't matter.
  
  user14180: You could try mxfold2.
  https://github.com/mxfold/mxfold2
  % mxfold2 predict test.fa
  >DS4440
  GGAUGGAUGUCUGAGCGGUUGAAAGAGUCGGUCUUGAAAACCGAAGUAUUGAUAGGAAUACCGGGGGUUCGAAUCCCUCUCCAUCCG
  (((((((........(((((..((((.....))))...)))))...................(((((.......)))))))))))). (24.8)
  
  
original_text: 16811: <p>I want to manually fold and pair two sequences (U4 and U6). And I want to make niceish figures.</p>
  <p>I haven't found a single program that does that.</p>
  <p>thanks</p>
   3848: <p>The RNA viewer that is particularly good is <a href="http://varna.lri.fr" rel="nofollow noreferrer">VA RNA</a>. This stands for &quot;Visualisation Applet for RNA&quot;. Its a java app and run it via,</p>
  <pre><code>java -jar /Route2Progam/vaRNA/VARNAv3-93-API.jar
  </code></pre>
  <p>Where <code>Route2Progam</code> is the path to where the jar files is stored, all other info in the run code is literal.</p>
  <p>Very nice pictures, point and clicky, drag structures into different shapes and easy to colour ... so for a GUI its great.</p>
  <p>They recommend <a href="http://wilab.inha.ac.kr/pseudoviewer/" rel="nofollow noreferrer">PsuedoViewer</a> for psuedoknots, but if that doesn't mean much ... it doesn't matter.</p>
   14180: <p>You could try mxfold2.
  <a href="https://github.com/mxfold/mxfold2" rel="nofollow noreferrer">https://github.com/mxfold/mxfold2</a></p>
  <pre><code>% mxfold2 predict test.fa
  &gt;DS4440
  GGAUGGAUGUCUGAGCGGUUGAAAGAGUCGGUCUUGAAAACCGAAGUAUUGAUAGGAAUACCGGGGGUUCGAAUCCCUCUCCAUCCG
  (((((((........(((((..((((.....))))...)))))...................(((((.......)))))))))))). (24.8)
  </code></pre>
  