Re: [modeller_usage] alignment matrix

[Modeller Caretaker <>]

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
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