ML estimation of model parameters
This protocol is extracted from research article:
Amino acid exchangeabilities vary across the tree of life
Sci Adv, Dec 4, 2019; DOI: 10.1126/sciadv.aax3124

For each alignment of two coding sequences, the program codeml in PAML4.9 was used to estimate ω under a user tree of two taxa, free parameters of individual codon frequencies, free parameter of κ, NSsites = 0, and no constraint of molecular clock. The control parameter aaDist was set to be 7 to allow the estimation of 75 individual ωij values.

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