Evolutionary rate analysis

• Codon dN/dS - Pairwise synonymous and nonsynonymous substitution-rate estimates

• Covarying evolutionary rates - Detect covariation in evolutionary rates

• Episodic rate covariation - Localize coordinated gene-rate shifts to reference-tree clades

• Projected covarying rates - Topology-robust rate covariation by reference-edge projection

• Relative rate test - Relative rate test between lineages