Compensatory mutations between protein residues that are in physical contact with each other can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment  ...  We have developed CCMgen, the first method for simulating protein evolution by providing full control over the generation of realistic synthetic MSAs with pairwise statistical couplings between residue  ...  CCMgen, a method for generating realistic synthetic protein sequence alignments whose residues obey the selection pressures de-85 scribed by a MRF with pairwise statistical couplings between residue positions  ... 

Compensatory mutations between protein residues in physical contact can manifest themselves as statistical couplings between the corresponding columns in a multiple sequence alignment (MSA) of the protein  ...  Fifth, we demonstrate how CCMgen and CCMpredPy can facilitate the development of contact prediction methods by analysing the systematic noise contributions from phylogeny and entropy.  ...  Synthetic protein alignments by CCMgen Third, we run CCMpredPy on each of the synthetic MSAs and predict residue-residue contacts by ranking the pairs according to the descending raw contact scores  ...