printing GTR rate matrix after optimization in HBL

[EHC2019]

Hi, Sorry for the basic questions. I hope this is the right place. I want to print the final rate parameters, how can I edit the GTR.bf file to print the estimated rate matrix? Also what are the order of parameters in paramValues? Can you please point me to the right place to learn more. Thank you! Einat

[spond]

Dear @EHC2019,

Can you elaborate on which GTR.bf you are referring to?

Best, Sergei

[EHC2019]

I apologize I meant REV.bf here https://github.com/veg/hyphy/tree/master/Examples/SimpleAnalyses

[spond]

Dear @EHC2019,

Ah, right. Those some old files :)

The REV.bf file estimates a per-branch REV model, so you have different rate matrices for each branch, so printing the estimates is a bit involved (see attached).

As far as paramValues go, you can use GetInformation to retrieve the name of the i-th parameter for a likelihood function, e.g.

for (k = 0; k < Columns (paramValues); k+=1) {
    GetString (parameter_name, theLnLik,k);
    fprintf (stdout, parameter_name, " = ", paramValues[0][k], "\n");   
}

Best, Sergei

REV-print.bf.zip

[EHC2019]

Thank you, Sergei It seems that I need to ask the question better. :-)

I have a known tree and an MSA and would like to estimate the R/Q matrix. I would like to do that with GTR (probably late with nonGTR model). I would like one to start with one matrix per tree (not per branch). Which file/s I have better start with and should I print the matrix the same way :-) Thanks!

[spond]

Dear @EHC2019,

Ah, for something like that you could use something like https://github.com/veg/hyphy-analyses/tree/master/NucleotideNonREV -- a pre-written analysis.

Best, Sergei

[EHC2019]

Thanks, I will try it. Will it print the rate matrix?

[spond]

Dear @EHC2019,

Yes (check the README for more examples).

Best, Sergei