Below is the previous post content, but I've just reformatted all this to a list now for easier future reference.
Looking for suggestions for tools generating nice viz outputs for various biological sequence data (e.g. plotting genome tracks with features).
So far I've come across:
They aren't quite as fully featured as I'd like (and BioGrapy is actually broken). Ideally I'd like programmatic tools (and python would be nice!), though GUIs are fine too. I have typically used ARTEMIS and SnapGene in the past, but they have little to no customisability.
Anyone come across things they really like?!
Some more I've come across from speaking to some other people!
GenoPlotr (An R solution)
GenomeDiagrams (part of BioPython already which is nice)
I’ll add that, since these are going to be going in to a LaTeX doc, TeX packages are fair game too! I really like TeXShade for multiple sequence alignments for instance