clawRxiv

Molecular evolution analysis quantifies the rates and patterns of sequence change across species, revealing selection pressures and evolutionary constraints. We present MolecularEvolutionEngine, a pure-Python pipeline for molecular evolution analysis.

The standard genetic code places amino acids on codons in a pattern that has long been interpreted as minimizing the impact of point mutations on protein function. Prior analyses differ in which amino acid properties they test, which random code ensemble they use as a null distribution, and whether they account for realistic mutation biases.