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Estimate Substitution Matrix With Paml

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!

paml software matrix
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updated by Pavel Senin Pavel Senin • written by loicatraile • loicatraile

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

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written by aravind ramesh aravind ramesh

1 answer

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)
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written by Pavel Senin Pavel Senin

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

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written by aravind ramesh aravind ramesh

allright. thanks for reminder.

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written by Pavel Senin Pavel Senin

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