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.

Dear jxn,

You can use HarvestFrequencies to compute frequencies from the data (take a look at Examples/SimpleAnalyses/F81.bf in the HyPhy directory for a very basic example), or you can define it by hand, e.g.

[code]
obsFreq = [0.4}{0.2}{0.2}{0.2]
[/code]

Cheers,
Sergei

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

Dear jxn,

You have a typo in [code]Model REV = (REVRateMatrix, obsFreq); [/code] - the second argument should read obsFreqs

Cheers,
Sergei