I've rejigged the "example inferred ARGs" section quite a bit here. Basic ideas:
I tried to make the paragraphing more logical, with clear ideas in each one
The method descriptions in the figure caption weren't very enlightening, so I moved them into the text to allow for a reasonable summary. We still need a description of Relate, which I'm hoping Ana will do.
I've tried to cut down the number of things we're discussing to something manageable, so the reader has some chance of digesting it.
I've rejigged the "example inferred ARGs" section quite a bit here. Basic ideas: