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.

Hi krwollen,

Our Bugzilla instance has fallen into disuse, sorry about this. I'll make sure the mail server settings are updated so that it can send out the mail.

Thanks for the bug report; I think I have fixed the problem now, and it will be pushed out with the next code update.

Sergei