Citation
Barrantes-Reynolds, R., Bond, J.P., & Wallace, S.S. (2011). Using Shifts in Amino Acid Frequency and Substitution Rate to Identify Latent Structural Characters in Base-Excision Repair Enzymes. PLOS ONE, 6(10), e25246.
Summary
First author paper! In bioinformatics analysis one commonly uses the amino acid as the unit of analysis (for phylogenetics, alignment, etc), as it is easier statistically. We used amino acids that were grouped together in the structure as the unit, with mutation rate as the character to do analysis on. Thanks to this we identified an important ancestral edge in the phylogeny, and this worked also served as the basis for my thesis, in which we did Bayesian statistics on alignments, trees and protein structures using these ideas.
