Mindmap works great for me especially for creative process. My personal choice is Freemind. It's easy to automate anything with freemind files because it's simple XML. I have a few scripts that allow me extract necessary information from big mindmaps: https://github.com/mrjazz/freemind-tools-python
I would also highly recommend Freemind, and in particular, learning to use keyboard shortcuts for creating new siblings, parents, navigating and deleting etc. You should not need to use your mouse for anything.
