Molecular biology is organized hierarchically: proteins form complexes which create pathways and meta-pathways that influence phenotype. Characterizing this hierarchy in a general way is difficult due to the complexity of genomes.
SCALES is a framework that analyzes patterns of co-variation amongst genomic features across a diversity of bacteria to infer a hierarchy of statistical interactions between proteins. The statistically derived hierarchy of molecular interactions reflects the hierarchy of biological function across different pathways in different bacterial organisms. In brief, given a genotype, SCALES provides a hierarchy of protein interactions that are relevant to understanding phenotype.