pyRSD-CoEv

pyRSD-CoEv identifies genes undergoing selective sweeps and detects coevolutionary gene clusters from genomic variant data to enable analysis of selection and coevolutionary processes in populations of closely related breeds or individuals without replicates.

Key Features:

• Selective Sweep Detection: Uses relative homozygous single nucleotide variant density (RSD) to identify genomic regions affected by selective sweeps.
• Coevolutionary Gene Cluster Identification: Detects clusters of coevolving genes by analysing correlated evolutionary rates among genes.
• Single-individual per breed analysis: Operates on populations of closely related breeds or individuals from distinct species without requiring replicates to detect selection signals.

Scientific Applications:

• Genetic basis of complex traits: Linking selective sweeps and coevolving gene clusters to genes underlying complex phenotypic traits.
• Selection and coevolution studies: Investigating artificial selection and natural coevolutionary dynamics across closely related populations or species.

Methodology:

Implements two analysis workflows: Selective Sweep Identification using RSD to pinpoint regions with elevated relative homozygous single nucleotide variant density, and Coevolutionary Gene Cluster Analysis using correlated evolutionary rates to detect clusters of coevolving genes.