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Table 3 Analysis of a large phylogenomic data set [29] consisting of 133 proteins from 40 taxa, 24294 sites for two competing trees under single frequency model and cF mixture model.

From: A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

Tree Single frequency model (JTT + F + Γ) Class-frequency mixture model (JTT + cF + Γ)
Microsporidia plus archaea clan -745,292.15* -738,445.15
Microsporidia plus Fungi clade -745,366.62 -738,371.59*