Data from: Modeling site heterogeneity with posterior mean site frequency profiles accelerates accurate phylogenomic estimation

Huai-Chun Wang, Bui Quang Minh, Edward Susko & Andrew J. Roger
Proteins have distinct structural and functional constraints at different sites that lead to site-specific preferences for particular amino acid residues as the sequences evolve. Heterogeneity in the amino acid substitution process between sites is not modeled by commonly used empirical amino acid exchange matrices. Such model misspecification can lead to artefacts in phylogenetic estimation such as long-branch attraction. Although sophisticated site-heterogeneous mixture models have been developed to address this problem in both Bayesian and maximum...
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