Joomla Auto Category Tree Menu provides you ability to insert auto generated menu instead of standard manually constructed menu.
This module is the best sulution if you want to replace standard Joomla menu with automatical one and when you want to fully customize it by your CSS and JS.
After you customized menu, is generates with using valid pure HTML. No JS or CSS comes with module: it is a task for your Joomla template. But we have the example of flexible configuring this menu.
All of menu nodes can be configure with CSS. Module marks all menu items with a log of CSS styles you can define in your CSS file. Some of them are: "selected", "child-of-selected", "article", "category", "level-0", "level-1" etc.. You can read more about it on according documentation page.