CladePP

CladePP detects local gene coevolution across multiple evolutionary scales to map gene function and identify novel pathway components such as in the homologous recombination repair (HRR) pathway.

Key Features:

• Local Coevolution Detection: Detects coevolutionary relationships between genes across hundreds of genomes using phylogenetic profiling.
• Multiscale Analysis: Determines the evolutionary scale of coevolution from clade-specific levels (e.g., mammals, vertebrates) to broad groups (e.g., animals, plants).
• Enhanced Predictive Power: Improves sensitivity and biological relevance in predicting gene function and pathway membership compared to traditional phylogenetic profiling methods.

Scientific Applications:

• HRR pathway mapping: Identified novel genes that coevolve with components of the homologous recombination repair (HRR) pathway across eukaryotes and within specific clades.
• Functional validation: Functional assays confirmed roles of eight newly identified genes in DNA repair at cellular and organismal levels.
• Disease and gene function prediction: Enables prediction of gene functions and identification of novel factors related to genetic disorders and cancers associated with HRR defects.

Methodology:

Phylogenetic profiling that leverages local coevolution signals across extensive genomic datasets to pinpoint the evolutionary scale at which coevolution occurs.