Merge pull request #2406 from RosettaCommons/ch.norn@gmail.com/alignmentCleaner
AlignmentCleaner filters -- useful for removing epistasis from MSAs. Typically, to learn the amino acid background frequencies for a protein one would assume that all the sequences in a MSA are samples from some average amino acid frequency profile. However, knowing a structure of your target sequence, this is assumption is unnecessary. Instead you could make sure, that each amino acid in the MSA is a sample from the same chemical environment as your target sequence.
This is useful for optimizing the force field and possibly also for design.