I'm dealing with a protein that has both ordered and disordered regions (most of it is disordered). I need to align this protein with very high accuracy (I don't care much about speed) with 40 of its orthologs, in a multiple sequence alignment. I want both ordered and disordered regions to be aligned properly, so I do not want to depend on substitution models. What would you recommend? MAFFT? MUSCLE?
As an aside, is some of you aware of a substitution model available for intrinsically disordered proteins? The only one I know of can be found here.