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sanger-pathogens / Roary

Rapid large-scale prokaryote pan genome analysis
http://sanger-pathogens.github.io/Roary
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Question: what programs can be used to visualize embl and dot files? #394

Closed karinlag closed 6 years ago

karinlag commented 6 years ago

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 commented 6 years ago

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

andrewjpage commented 6 years ago

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

karinlag commented 6 years ago

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 :smiley:

andrewjpage commented 6 years ago

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 commented 6 years ago

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