Does anybody knows how to estimate an amino acido substitution matrix using the PAML software? I´m not getting anywhere.. any suggestions woulds be really apreciated.. thanks!
Do you want to generate a substitution matrix from a set of proteins ?
Will this help, 'Bayesian molecular dating using PAML/multidivtime'?
Excerpt from the manual:
Step 3: Estimation of model parameters
Obtain estimates for
• unequal nucleotide frequencies
• transition/transversion rate ratio: parameter κ
• rate heterogeneity among sites: shape parameter α (discrete γ model of rates among sites)
This is not an answer. Its a comment. Little explanation makes an answer.
allright. thanks for reminder.
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