On 07/25/2011 12:38 AM, Ashish Runthala wrote: > Tell me the solution to a query. Suppose I have 4 templates for a > target sequence. And while using salign_multiple.py, I want to start > the progressive alignment specifically from template 2 only, to let > others follow this template2 alignment. Tell me the way to make > salign force the progressive alignment starting on from a specific > template only?

Progressive alignment aligns each sequence to the first sequence in the alignment, so simply put template 2 first in your alignment file (or list the align_codes explicitly when you read in the alignment file, and put template 2's align code first in that list).

Ben Webb, Modeller Caretaker