Question: Estimate Substitution Matrix With Paml
0
gravatar for loicatraile
5.6 years ago by
loicatraile40
Germany
loicatraile40 wrote:

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!

software matrix paml • 1.7k views
ADD COMMENTlink modified 5.6 years ago by Pavel Senin1.9k • written 5.6 years ago by loicatraile40

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

ADD REPLYlink written 5.6 years ago by aravind ramesh510
0
gravatar for Pavel Senin
5.6 years ago by
Pavel Senin1.9k
Los Alamos, NM
Pavel Senin1.9k wrote:

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)
ADD COMMENTlink modified 5.6 years ago • written 5.6 years ago by Pavel Senin1.9k

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

ADD REPLYlink modified 5.6 years ago • written 5.6 years ago by aravind ramesh510

allright. thanks for reminder.

ADD REPLYlink written 5.6 years ago by Pavel Senin1.9k
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