Table 1.

Methods for Comparing Selection among Different Sets of Branches.

Method	Application	Statistical Framework
Yang (1998)	Gene-wide differences in average ω	ML, LRT
Baker et al. (2016)	Gene-wide differences in distributions of ω	Random effects ML, LRT
Wertheim et al. (2015)	Gene-wide differences in distributions of ω	Random effects ML, LRT
Tamuri et al. (2012)	Site level amino acid preferences	Fixed effects ML
Murrell et al. (2012)	Site level directional selection	Fixed effects ML, LRT
Parto and Lartillot (2017)	Site and branch-level amino acid preferences	Bayesian MCMC mixture
	ω variation at site/branch level
Jones et al. (2020)	Gene-level phenotype—selection correlation at a fraction of sites	Random effects ML, ancestral state sampling, LRT, empirical Bayes
Contrast-FEL	Site-level differences in ω between sets of branches	Fixed effects ML, LRT

Note.—ML, maximum likelihood; LRT, likelihood-ratio test; MCMC, Markov Chain Monte Carlo.