... likely noise Addressing this limitation is an important area for continued effort Data availability Data are available upon request Abbreviations BFS, breadth-first search; CC, co-conservation; ... million years ago (MYA) from O157, an estimated 100 MYA from Salmonella, 200 MYA from Pseudomonas, and 1,200 MYA from Bacillus Thus, we examined a combination of pathogenic and non-pathogenic organisms ... its ability to analyze only a single species at a time In contrast, CS-CCC examines each cluster across multiple species and reveals interactions that both homology-based methods and CCC fail...