I have recently installed MacOSX Lion and thus needed to install MrBayes v3.2. Unfortunately Mr Bayes v3.2 has altered the output tree format to an exotic nexus format. Archeopteryx refuses to open the files claiming that there is no closing "]". However, FigTree and Geneious open the Bayes ouput and show the posterior probabilities albeit replaced to the baranches rather than the nodes where they were in Mr Bayes 3.1.2. Unfortunately when exporting the trees from these latter programs, Archeopteryx again refuses to open the files claiming that there is no closing "]". The only outputs (exports) Archeopteryx now opens are those without posterior probabilities. Sadly this makes Archeopteryx obsolete for my workflow. Does anyone have any solutions?
For me Archeopteyx is superb, and I really want to continue using it.