...
By default, a phylogenetic tree is synchronized with the corresponding alignment.
To disable/enable synchronization use the Tree and Alignment synchronization button. 
To load a tree from a file follow the instruction described in the Opening Document paragraph or use the Tree settings tab of the Options Panel. For example, you may open the $UGENE\data\samples\Newick\COI.nwk sample file provided within UGENE package.
...