I have a question about the example script salign.py in the Advanced tutorial for version 8v2. I understand the logic of the script where salign is called three successive times incorporating more information each time in the form of the "weights" parameter, and one sees increase in alignment quality with each cycle. However, I am unclear of the purpose of the last call to salign after the alignment files are written. The tutorial text says that the last call is to generate a quality score, but after examining the log file the quality of the alignment after this call is worse than after the first three calls. I noticed that the rms_cutoff for the first three calls is 3.5, while that for the final call is 1.0 (presumably more stringent), and that the alignment type is "progressive" rather than "tree." Since the alignment files are already written, and this is what is used in the alignment with the sequenced to be modeled, why is this last step run?

As usual, thanks for all of your help

Mike White