Sometimes you might want to remove the dependencies with the software itself.In this case you should use the command
apt-get autoremove. It will remove packages that are installed as automatic dependencies, but are not depended anymore.
Apt-get has a flag –auto-remove that can be used to automatically remove the automatically installed packages when removing a manually installed package:
apt-get remove --auto-remove packagename
Certain other tools are also capable of doing this, for example aptitude will automatically suggest that you remove the packages that have been orphaned.
The automatically installed packages tracking is built in to apt so the tracking should work no matter which tool you use to install the packages.