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In recent years, increasing attention has been placed on the development of phylogeny-based statistical methodologies for uncovering site-specific changes in amino acid fitness profiles over time. The few available random-effects approaches, modelling across-site variation in amino acid profiles as random variables drawn from a statistical law, either lack a mechanistic codon-level formulation, or pose significant computational challenges.doi:10.1186/s12862-019-1358-7 pmid:30808289 pmcid:PMC6390532 fatcat:flg7i63c3rff5f7ldquxxpzoya