Diapositiva 1

CODEML.ctl parameter file
• Ziheng Yang: Computational Molecular Evolution
• PAML User Guide
k → transition/transversion rate ratio
π → codon frequency
• Yang Z, Nielsen R. Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary
models. Mol Biol Evol 2000; 17: 32-43
• Yang Z. PAML 4: phylogenetic Analysis by Maximum Likelihood. Mol Biol Evol 2007; 24: 1586-1591
• F EQUAL: each codon has the same frequency
• F1X 4: codon frequency are expected from the
frequencies of four nucleotides.
• F3 X 4: codon frequencies are expected from 3
sets of nucleotide frequencies for the three
codon positions.
• F61: all codon frequnecies as parameters