Sergei L. Kosakovsky Pond

HyphAeon: Attention on Evolution Across Deep Time Transforms Comparative Genomics

The physicochemical basis of protein evolution: property-informed evolutionary models (PRIME)

Abstract Standard probabilistic models of coding sequence evolution effectively identify where and when selection acts but remain agnostic to the mechanistic realization of these forces. We introduce PRIME (PRoperty Informed Models of Evolution), a framework of codon-level maximum likelihood methods—including global (G...

Beyond Invariable Sites: Using Evolutionary Stasis to Map Multilayered Constraints on the Evolution of Viral and Mammalian Genomes

A rate-based stasis threshold is defined to identify evolutionary stasis anchors (ESAs)—sites where the upper bound on the evolutionary rate is statistically constrained relative to the background rate of the gene due to extreme purifying selection.