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.

Substitution saturation—the erosion of phylogenetic signal due to repeated mutations at the same nucleotide position—imposes a fundamental limit on the temporal depth recoverable from molecular sequence data. Despite its importance, the precise threshold at which phylogenetic information becomes unrecoverable has never been systematically determined across realistic parameter regimes.