I am going to align a bunch of protein sequences using ClustalX2. This software first builds a guide tree from pairwise distances between sequences and uses that tree for multiple alignment of sequences. I need to know the order of sequences which are chosen for alignment via the guide tree. ClustalX2 by default uses neighbor-joining algorithm to create the guide tree and stores the tree in a .dnd file. But when I visualize the tree it seems it is unrooted because it has three branches in its first level.
The following picture shows my tree that ClustalX2 stores in a .dnd file:
1- How do I know this tree is rooted or unrooted?
2- If this tree is unrooted how ClustalX2 uses it as guide tree? As far as I know the guide tree should be rooted.