Using the msa package, I did a multiple alignment of 3 highly similar sequences, each of length ~8 kb.
I then tried to print them to an image using the msaPrettyPrint function.
LaTeX complains about exceeding the input stack size = 5000
nevermind. i see now the part of the vignette describing breaking the alignment into chunks, with the numbering restarting for each chunk. my apologies.
Of course, that is exactly what I would have answered. If you have any other questions or issues, please let us know. All the best!
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