To check the number of marked species
look at the button in the ARB_NT top area displaying the number of all marked species or
choose one of the various 'Count marks of .. species ..' from the 'Mark species' menu.
The "current tree" mentioned above is the tree currently displayed in the main window. When you have multiple ARB_NT windows open (see ´Multiple ARB_NT windows´), make sure you use the menu of the intended ARB_NT window.
When using one or two sets (tree, complete, partial or alignment), all species not included in the set (or in both sets) will not be affected/counted.