Answers.Body: <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.sstatic.net/XDZ3T.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/XDZ3T.png" alt="enter image description here"></a></p>
  
  <p><a href="https://i.sstatic.net/Hr7OY.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/Hr7OY.png" alt="enter image description here"></a></p>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2017-11-10T21:34:53.757Z
Answers.LastActivityDate: 2017-11-10T22:27:08.123Z
Answers.LastEditDate: 2017-11-10T22:27:08.123Z
Answers.UserDisplayName: quantik
Body: <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>
  
Tags: <phylogenetics><methylation><visualization>
Title: Highlight CpG sites with Texshade
ThreadText: # Highlight CpG sites with Texshade
  
  (Asked by: username_0 on 2017-11-10)
  
  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!
  
  **Tags:** phylogenetics, methylation, visualization
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_0 on 2017-11-10. Score: 4 | Accepted answer
  
  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.
  [![enter image description here](https://i.sstatic.net/XDZ3T.png)](https://i.sstatic.net/XDZ3T.png)
  
  [![enter image description here](https://i.sstatic.net/Hr7OY.png)](https://i.sstatic.net/Hr7OY.png)
  
  
  ---
  
  