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Non-Negative Matrix Factorization for Learning Alignment-Specific Models of Protein Evolution

Figure 8

Likelihood improvement predicts phylogenetic difference.

The difference between phylogenies increases as the mean likelihood difference per site between NNMF and WAG increases. , (, randomization test with replicates). Assuming intercept of 0, slope = 38.1. Without this assumption, intercept = −0.31, slope = 38.5.

Figure 8