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