So I am using Texshade to show similarities in a MSA (Multiple sequence alignment). I am mostly interested in the alignment of the CpG sites (i.e. where the CG pair of nucleotide). I am not sure how to go about displaying the MSA with only the CG pairs highlighted. I have tried using the \DNAgroups command with {CG} but this does not seem to work. If anyone has any suggestion on how to do this that would be very much welcomed. Here is my current .tex file:











Another remark: I am using the R package msa is create this .tex file.


1 Answer 1


enter image description hereThe 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.


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