*** ERROR ***  MSA::GetLetter(0/1, 152/24551)='

This bug has proved to be very difficult to isolate, and I have given up trying to fix it. Fortunately, it appears to be quite easy to work around with a little bit of trial and error. Small changes to the way MUSCLE is run usually avoid the crash. This could be changing the order of the input sequences, running with fewer -maxiters, running a 32-bit instead of 64-binary or vice versa, changing a parameter such as a gap penalty by a very small amount, and so on.