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Re: [modeller_usage] I need some information about an salign module

On 8/15/11 9:33 AM, Ashish Runthala wrote:

The script salign_multiple_struc.py works on
sub-optimal alignments as given on page
http://computing.bio.cam.ac.uk/local/doc/modeller/node294.html

Tell me, is this script similar to the consistency and sub-optimal
alignment generation, as cited by Travis Wheeler for MAFFT, PROBCONS,
TCOFFEE.
Without a reference, the best I can do is tell you how Modeller's suboptimal alignment generation functions, and you can compare the algorithms yourself:
After finding the optimal path through the alignment matrix by dynamic programming, subopt_offset is added to each matrix position on the path and the path reevaluated. Typically this results in a different (sub-optimal) path being found. 

	Ben Webb, Modeller Caretaker
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