You can uninstall or removes an installed autogen package itself from Ubuntu 16.10 (Yakkety Yak) through the terminal,
$ sudo apt-get remove autogen
If you would like to remove autogen and it's dependent packages which are no longer needed from Ubuntu,
$ sudo apt-get remove --auto-remove autogen
If you use with purge options to autogen package all the configuration and dependent packages will be removed.
$ sudo apt-get purge autogen
If you use purge options along with auto remove, will be removed everything regarding the package, It's really useful when you want to reinstall again.
$ sudo apt-get purge --auto-remove autogen