Molecular evolution analysis engine for dN/dS ratio estimation, codon substitution modeling, phylogenetic signal detection, and rate heterogeneity analysis.
- Codon-level dN/dS ratio estimation across gene families
- Positive selection detection using branch-site models
- Phylogenetic signal quantification (Blomberg's K, Pagel's lambda)
- Rate heterogeneity modeling with gamma distribution
- Molecular clock calibration and divergence time estimation
200 genes × 20 species; Mean dN/dS=0.458; 27 pos. sel. genes; Clock r²=0.978
pip install numpy scipy matplotlib
python molecular_evolution_engine.pymolecular-evolution, dnds-ratio, codon-evolution, phylogenetic-signal, rate-heterogeneity