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!
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1 Answer
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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.
