<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>

CC BY-SA 3.0
2017-11-10T21:34:53.757Z
2017-11-10T22:27:08.123Z
2017-11-10T22:27:08.123Z
quantik
<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>

<phylogenetics><methylation><visualization>
Highlight CpG sites with Texshade
# 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

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## 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.


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