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So I'm actually doing, for the first time, actual routing for an actual run of my actual own. It's got some nuances and several branches that are slightly different from one another that seem to get kind of twisty. Does anyone have examples of how they tackled the problem in any way that's better than just a .txt with indents?
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Not speedrun-specific, but I discovered a graph program called Graphviz with which you can visualize trees beautifully for others. You input your nodes and properties with the dot code format. Not as good to edit live, though.

A graph I did with the sfdp layout looks like this:
I'll check it out! Ideally, there should be live editing so that you can, e.g. overlay it on top of a map and make it neat, also so you can change values. I guess I've never seen a map like that... but there has to be some tool that can do it. Perhaps there's even calling for something that finds the total time for each route and shows the fastest route for you based on your data. Ofc it's never gonna be reliable unless your testing and timing was perfect, and only more complex games need it anyway.
Soulless Killing Machine
Looked at it briefly but it seems to be a tool that reads text files.  Is there a graphical interface for this where I can kind of drag and drop nodes? 
Haven't tried one, but there seem to be a lot of programs that might be able to just do that: http://www.graphviz.org/content/resources
I have only used graphviz with programmatically generated code.