text: user712: I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? If not is there another MSA visualizer I can use that can produce a figure like this. Thanks! 
  
  user712: The best solution I could find was to use the \shaderegion function on all the sequences so it ended up looking something like this:
  \shaderegion{1}{CG}{Red}{OrangeRed}
  
  \shaderegion{2}{CG}{Red}{OrangeRed}
  
  ...
  
  Then I cast the rest of shading similarity to grey so the CG pairs were more easily distinguishable.
  \shadingcolors{grays}
  
  Two examples one with \fingerprints and one regular.
  
  
  
original_text: 712: <p>I am using Texshade to produce figures for MSA. Upon reading the documentation I could not find anyway to highlight how conserved CpG sites within the alignment. Does anyone know if this is possible? If not is there another MSA visualizer I can use that can produce a figure like this. Thanks! </p>
   712: <p>The best solution I could find was to use the <code>\shaderegion</code> function on all the sequences so it ended up looking something like this:</p>
  
  <pre><code>\shaderegion{1}{CG}{Red}{OrangeRed}
  
  \shaderegion{2}{CG}{Red}{OrangeRed}
  
  ...
  </code></pre>
  
  <p>Then I cast the rest of shading similarity to grey so the CG pairs were more easily distinguishable.</p>
  
  <pre><code>\shadingcolors{grays}
  </code></pre>
  
  <p>Two examples one with <code>\fingerprints</code> and one regular.
  <a href="https://i.stack.imgur.com/XDZ3T.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/XDZ3T.png" alt="enter image description here"></a></p>
  
  <p><a href="https://i.stack.imgur.com/Hr7OY.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/Hr7OY.png" alt="enter image description here"></a></p>
  