Hello all, I have a simple question where I did not find an answer, yet - explained with an example: Assuming one has an aligment, consisting of 2 partitions, and at the second partition sequences are not available, so that these lines are filled with "-" or "?" only. And then one makes a best fit model test for the second partition - first WITHOUT these sequences and then WITH these empty sequences - would that change the best fit model? All the best Dieter