A friend of mine (he is a physicist) just asked me if I have a standard way of texing DNA sequences. I do not have one but was curious for a good solution.
Anyone has a good solution to this? It should have publication quality. Coloring and marking specific subsequences should be possible.
If you have one not using LaTex: Feel free to add.
From the TeXshade README file: TeXshade is an alignment shading software completely written in TeX/LaTeX which can process multiple sequence alignments in the MSF, ALN and FASTA file format.
I have happily used it in the past, although large alignments were likely to cause issues (but that was many years ago).
I am pretty sure alignments are covered in the LaTeX companion, however, it's been a few years and I could be wrong. Personally I would avoid LaTeX for this (too complicated) and simply render sequences in SVG.
I don't believe there is a standard solution, or very many packages aimed at sequence formatting in LaTeX. Most people would roll their own, using their knowledge of LaTeX.
This is a few years old but might be useful for other purposes:
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There are nice packages for alignments but I am not looking for alignments.