I just started using the WebStart version of TreeJuxtaposer. Section 2.4 of your ReadMe file says that files can be in NEXUS format. When I try to open a standard NEXUS file, (exported from PAUP* without branch lengths, and in ALTNEXUS format), the program hangs. Not only no error messages, but also will not close, so have to kill the job. I have wasted an hour on this, but discovered that your sunflower example works with just a tree.
So, I copied out just the tree, and now I can start to see the good things you have written.
There is plenty of entropy in the universe, and no need for software to create more. Trapping an unreadable file with an error message would be a great addition!