Relative character-state space, amount of potential phylogenetic information, and heterogeneity of nucleotide and amino acid characters.

Abstract excerpt

We examined a broad selection of protein-coding loci from a diverse array of clades and genomes to quantify three factors that determine whether nucleotide or amino acid characters should be preferred for phylogenetic inference. First, we quantified the difference in observed character-state space between nucleotides and amino acids. Second, we quantified the loss of potential phylogenetic signal from silent...

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