Question: what programs can be used to visualize embl and dot files?

[karinlag]

According to the documentation, it says that these files can be used for visualizaton. My google foo is having very limited success regarding finding software that I can input these to. Could you give me any tips in this regard?

[andrewjpage]

Artemis can visualize embl files. Lots of graph programs can visualize dot files, the one I use is gephi

[andrewjpage]

You can also pop the output into phandango or panx to interactivity view data

[karinlag]

So, I tried putting a core_accessory.header.embl into Artemis, and it fails, saying the 'entry contains no sequence'. Are there options to roary that I'm not using, and/or other ways of working around this?

And thanks for the tips regarding gephi and phandango/panx 😃

[andrewjpage]

With Artemis load in the core gene alignment FASTA file, then add the annotation (embl or gff) on top. I think you load the annotation under File->Add Entry.

[karinlag]

@andrewjpage Thanks so much for this, this helps a lot!