CladePP

CladePP is a software tool that uses clade phylogenetic profiling to identify gene functionally linked to a specific biological pathway, such as the homologous recombination repair (HRR) pathway. The tool analyzes the coevolution of genes across hundreds of genomes at different evolutionary scales, such as mammals, vertebrates, animals, and plants. By detecting local coevolution patterns, CladePP can identify genes coevolved with the pathway of interest globally across all eukaryotes or locally in specific clades.

The developers of CladePP demonstrated its effectiveness by identifying dozens of previously unrecognized genes that coevolved with the HRR pathway. They validated eight of these genes through functional biological assays, confirming their role in DNA repair at both cellular and organismal levels. These newly identified genes are expected to contribute to a better understanding of the HRR pathway and may provide insights into missing heredity in HRR-associated cancers, such as hereditary breast and ovarian cancer.