A General Empirical Model of Protein Evolution Derived from Multiple Protein Families Using a Maximum-Likelihood Approach

• Good replacement matrices represent the relative rates of amino acid replacement at homologous sites in a protein in order to estimate the true evolutionary distances and relationships among species (pg 691)
• Maximum parsimony (MP) assumes that for any given site in an alignment, only one change takes place along any single branch in a tree, which can lead to underestimation of the true number of replacements that have occurred in branches where multiple changes have occurred and may lead to systematic error in any model estimated using counts of replacements. Dayhoff may be affected by this, JTT's attempt to reduce the impact of this problem are instead wasteful. (pg 691)

• Assumption: models in this paper assume all amino acid sites in an alignment evolve independently and according to the same Markov process.
• Assumption: Amino acid frequencies and the model of evolution are assumed constant through time and across all sites in alignment
• Assumption: Markov process assumed to be reversable, ie n_ij = n_ji