Hi folks, 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. This is the file I have for now: http://pwe.no-ip.org/other/modeller.txt If anyone could assist me a little or point me to the right direction I'd be glad. Thanks so far, Paul
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