hi, I am just starting Hyphy to define a model

for the vector obsFreqs, how can i define it?

here is my code

REVRateMatrix = {{*,a,b,c}{a,*,d,e}{b,d,*,f}{c,e,f,*}};
Model REV = (REVRateMatrix, obsFreq);

Thanks a lot.

Sergei, thank you for your reply.

I did put HarvestFrequencies in my code before. but it didn't work


Error:obsFreq has not been defined prior to the call to Model = ...
Current BL Command:Define the model REV using transition matrix REVRateMatrix and equilibrium frequencies.obsFreq

my code
-------------------------------------
DataSet myData = ReadDataFile ("/home/cmei/HyPhy/Hominoid.txt");
DataSetFilter myFilter = CreateFilter (myData,1);
HarvestFrequencies (obsFreqs, myFilter, 1, 1, 1);

REVRateMatrix = {{*,a,b,c}{a,*,d,e}{b,d,*,f}{c,e,f,*}};
Model REV = (REVRateMatrix, obsFreq);

Tree myTree = (Or((Mc,Gb)(Hm(Gr(Ch,Bo)))));

LikelihoodFunction theLikFun = (myFilter, myTree, obsFreqs);
Optimize (paramValues, theLikFun);
fprintf (stdout, theLikFun);
-------------------------------
Maybe i had other problems.

any specific struture of the sequence data in the data file?can it be .txt? and should the species name start with #?

Thank you so much