The Dayhoff Exchange Score: A new metric to quantify site saturation in amino acid datasets prior to phylogenetic analysis

Entropic site saturation is a persistent problem in phylogenetic analyses,
where it can hinder the accuracy of topology reconstruction. It is
fundamentally caused by large amounts of independent change along
branches, causing the model to be unable to distinguish phylogenetic
signal from noise. The Dayhoff Exchange Score (DE-score) is a new metric
to assess this form of site saturation within and between amino acid
datasets, which provides both a whole dataset overview and taxon-specific
values that represent the contribution of a given taxon to the whole
dataset entropic site saturation. We first assess the efficacy of this
score at detecting increased entropic site saturation over 20,000
simulation datasets, compare it to the existing Slope R2 score, and then
assess its efficacy in the face of the potentially confounding factors of
increasing taxon number, number of positions in the alignment, missing
data, and noise. Finally, we use the DE-Score to re-evaluate several
previously published datasets to illustrate its efficacy.