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 -- modeller-care@salilab.org http://www.salilab.org/modeller/ Modeller mail list: http://salilab.org/mailman/listinfo/modeller_usage