I try to run a Beast analysis on 2 genes: cytb and CR. I have run the analysis multiple times, and once the analysis has run, ESS and convergence look good in Tracer. However the output tree is odd. When opened in Figtree I can only view the tree if I convert it to a cladogram and I can’t obtain node ages or a scale axis.

When opening the file in Genious the same problem comes up. On scrutinising the tree file in a text editor, it seems that the source of the bug is that Beast hasn’t written the tree file correctly. The tree file begins with “(((“, but then no other “(“ nor “)” symbols appear at all! For most formats I know, we’d expect this to be full of such symbols (depicting the branches) and, critically, the number of “(“ symbols must be exactly balanced with the same number of “)” symbols.

What's wrong, and how to solve it? Many thanks!