What's your favourite way to create sequence logos from the command line or programmatically?
This is in response to a question at StackOverflow on making sequence logos in ggplot2. I looked here and was surprised that couldn't find the answer.
Ideally, the package would be easy to use but flexible enough to show different logo representations (e.g. scale height by frequency or by information content) and different alphabets (DNA, RNA, and amino acids).
We have our own way of doing this in the lab, and being a PI, I don't know what it is, but I would like to hear other options.