How To Define Gap Cost In A Stepmatrix?

Question

[Yongjie Zhang]

Hi all,

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.

Thanks.

Yongjie

P.S. The gaps are unambiguously aligned in my case and contain valuable information.

[Yongjie Zhang]

This post relates to C: transition/transversion stepmatrices, but are different focus.