Paul Wilhelm Elsinghorst wrote: > I have a problem getting the alignment of two sequences the way I want > it to be. Please have a look at this picture to see what I'm looking > for: > > http://pwe.no-ip.org/other/modeller.jpg > > I'd like to set up my alignment file in a way that the alignment done by > modeller gives exactly this result. I fiddeled with fixed_pos things but > couldn't get it to work, actually I didn't figure out how it really > works.

I'm not sure I get it - if you already know what your alignment is, why are you asking Modeller to produce a new alignment? You can just provide the existing alignment file to Modeller as an input.

If you're trying to use the salign_fix_positions example, you should use negative rather than positive values for fix_offsets - the defaults are inappropriate for most applications.

Ben Webb, Modeller Caretaker