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1 Models of nucleotide substitution; 2 Models of amino acid and codon substitution; 3 Phylogeny reconstruction: overview; 4 Maximum likelihood methods; 5 Comparison of phylogenetic methods and tests on trees; 6 Bayesian theory; 7 Bayesian computation (MCMC); 8 Bayesian phylogenetics; 9 Coalescent theory and species trees; 10 Molecular clock and estimation of species divergence times; 11 Neutral and adaptive protein evolution; 12 Simulating molecular evolution; Appendixes; References

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