Re: [modeller_usage] alignment matrix

Schulze, Diana wrote: > I made a model with modeller and used the function auto_align() to get > an automatic alignment. Now my question is the following: How can I find > out which matrix (BLOSOM 60,...) was used to build this alignment?

By default, if you don't set rr_file, the sequence alignments (align and malign) used by auto_align() use the AS1 matrix.

Ben Webb, Modeller Caretaker