These are my favorite tools to plan, plot, and write a novel.
This is the program I use to run a story idea through hits paces, strike a working synopsis, and create character arcs.
Early - Complete First Draft
This is the program I use in conjunctions with Scrivener, where I lay out the chapters and scenes - and have a bird's eye view of the beats and story.
First Draft - Final Draft
Made for novelists. I break my chapters into scenes, and Scrivener makes it easy to move scenes around. A learning curve for sure, but once you've figured out what works for your process, this is a powerful tool.