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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The best solution I could find was to use the \shaderegion function on all the sequences so it ended up looking something like this:




Then I cast the rest of shading similarity to grey so the CG pairs were more easily distinguishable.


Two examples one with \fingerprints and one regular. enter image description here

enter image description here


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