When I'm doing phylogenetic analysis, I want to define both transition/transversion stepmatrices and gap mode (to fifth base). But I found the Paup program always reported error and stopped. It gave such information:"One of more active stepmatrix definitions does not include costs for changes to the gap state. You must assign different types to these characters before changing the gap-mode setting". Or, "Character 117 is not compatible with usertype “2_1” (state '_' is not defined in the stepmatrix)".
My stepmatrix is like this:
usertype 2_1 stepmatrix = 4 acgt
'- 2 1 2 ( ' is added in the post to correctly display "-")
2 - 2 1
1 2 - 2
2 1 2 -
I realize my problem seems to be the conflict between gap mode and stepmatrix. But can I define a cost for gap in the stepmatrix? How to do that, and what cost value can be given to gap in the stepmatrix?
Please let me know if you have a solution.
P.S. The gaps are unambiguously aligned in my case and contain valuable information.