So far it seems like dagre-d3 is the best option for those that want directed graphs to be automatically redrawn (with transitions) based off of user input. I'm continually looking for better options, though.
viz.js is Graphviz recompiled to javascript with Emscripten. Dagre is the dot algorithm implemented in JS. I found dagre to work really well in most cases but Graphviz beats dagre in some edge cases (e.g. not order dependent, better with hierarchies, ...).
