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.

Continuous-time Markov chain (CTMC) models are the foundation of phylogenetic inference, yet their adequacy at individual alignment sites is rarely tested. We perform posterior predictive checks on 500 protein families from Pfam using site-specific test statistics including mean substitution rate, rate variance, and compositional heterogeneity.