To uninstall tree-puzzle-doc just follow these instructions.
/ubuntu/yakkety/universe///install/index.html Reconstruction of phylogenetic trees by maximum likelihood (doc) Ubuntu 16.10 universe/science 5.2-8build1
sudo apt-get remove tree-puzzle-doc
Which will remove just the tree-puzzle-doc package itself.
sudo apt-get remove --auto-remove tree-puzzle-doc
This will remove the tree-puzzle-doc package and any other dependant packages which are no longer needed.
If you also want to delete your local/config files for tree-puzzle-doc then this will work.
sudo apt-get purge tree-puzzle-doc
Or similarly, like this tree-puzzle-doc
sudo apt-get purge --auto-remove tree-puzzle-doc
|Description||Reconstruction of phylogenetic trees by maximum likelihood (doc)|