Both the app-text/tree and x11-libs/openmotif ebuilds create executables called /usr/bin/tree, whichever is installed last overwrite the previous copy. The x11-libs/openmotif tree seems to be a demo of openmotif, rather than anything vital to it's working so it might be easyest to either ot install it or change it's name.
obj /usr/X11R6/bin/tree 8fe153159e1480ecc8745eb3158381a8 1030633479 This is the line in my CONTENTS file which references tree. The latest ebuild of openmotif installs things /usr/X11R6 so /usr/bin/tree should no longer be overridden. emerge rsync emerge openmotif emerge tree path order will find /usr/bin/tree before /usr/X11R6/bin/tree so the system shouldn't be adversely affected by the binaries being installed at the same time.
