Known Bonsai bugs:

1) After the first multiple alignment a fatal error may occur in a large multiple alignment. Probably related to this, repetitions of the same alignment may not always be identical to the first (though they are very close), and multiple repetitions can eventually use up all the memory. These are all probably due to inadvertantly maintained object references, but they are hard to find.

2) Problem with C-terminal gap positioning such that they tend to avoid being at the alignment ends (this is a bad problem but I am having trouble figuring out why it happens).

2) Sequence lists may occasionally get corrupted. Validate Sequence List is a workaround.

3) Various minor visual interface problems.