KMAD was designed to align intrinsically disordered (aka natively unfolded) proteins for the HOPE mutation analysis server.
the Centre for Molecular and Biomolecular Informatics, the CMBI.
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KMAD: Knowledge based multiple sequence alignment for intrinsically disordered proteins.
Lange J, Wyrwicz LS, Vriend G.
Bioinformatics. 2015 Nov 14. pii: btv663.