I considered posting this through Bugzilla but they have not yet sent me my new account password (three hours after initiating the process), so here I am.

I recently performed a TestBranchDNDS.bf analysis and saved the resulting Syn and Nonsyn trees. When I viewed the saved trees in FigTree there were a few odd errors, including the second and fourth trees missing the most basal clade. After examining the tree file I realized the Newick trees were missing the semicolon at the end of each tree specification. Once I added this manually the trees were parsed correctly.