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By bridging statistical phylogenetics with geometric representation learning, HyphAeon establishes comparative genomics as an interactive, high-throughput computational framework for evolutionary discovery.
PRIME (PRoperty Informed Models of Evolution), a framework of codon-level maximum likelihood methods that explicitly model amino acid exchangeability as a function of physicochemical properties, provides a useful framework for characterizing the mechanistic drivers of protein diversity.
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.
A collection of over 3000 independent, full-length SARS-CoV-2 sequences deriving from posited or confirmed chronic infections is assembled and 14 distinct mutation patterns (MPs) that repeatedly appear in these sequences are described, including four CD8 T cell-escape MPs and two MPs that represent adaptation to tissue...
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