Estimate Substitution Matrix With Paml

Question

[loicatraile]

Hi all! 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!

[aravind ramesh]

Do you want to generate a substitution matrix from a set of proteins ?

Answer 1

[Pavel Senin]

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)

[aravind ramesh]

This is not an answer. Its a comment. Little explanation makes an answer.

[Pavel Senin]

allright. thanks for reminder.