Hi,

I am now using the hyphy windows version and I was wondering how to apply the same models and tests to many sets of alignments.


Nicholas

Hi Sergei,

I have two aligned sequences and i want to test whether the three codon sites evolve at equal rates.

So far I have the code below. Now I want to put a constraint in which sites 2 and 3 have the same branch length as site 1 and then compare the two optimized likelihood functions with an LRT. I will greatly appreciate if you help me with the coding ?  Thank you




DataSet myData = ReadDataFile ("C:/Users/bio/Desktop/example");


/* Create 3 filters: one for each of the
   three codon positions */

DataSetFilter myFilter1 = CreateFilter (myData,1,"<100>","0,1,3");
DataSetFilter myFilter2 = CreateFilter (myData,1,"<010>","0,1,3");
DataSetFilter myFilter3 = CreateFilter (myData,1,"<001>","0,1,3");


HarvestFrequencies (obsFreqs1, myFilter1, 1, 1, 1);
HarvestFrequencies (obsFreqs2, myFilter2, 1, 1, 1);
HarvestFrequencies (obsFreqs3, myFilter3, 1, 1, 1);


/* Define an HKY85 model using each of the 4 frequency sets */
/* Let R be the ts/tv ratio, which we will eventually allow to be shared by all three of the positions */
global R;

HKY85RateMatrix = {{*,b,R*b,b}{b,*,b,R*b}{R*b,b,*,b}{b,R*b,b,*}};
Model HKY851 = (HKY85RateMatrix, obsFreqs1);
Tree myTree1 = (a,b);
Model HKY852 = (HKY85RateMatrix, obsFreqs2);
Tree myTree2 = (a,b);
Model HKY853 = (HKY85RateMatrix, obsFreqs3);
Tree myTree3 = (a,b);



/* Analyze data using 3 partitions: each partition has separate rates and base frequencies, but the ts/tv ratio (R) is shared by all three. Also, each branch has the same ts/tv ratio. */


LikelihoodFunction theSplitLikFun = (myFilter1,myTree1,myFilter2,myTree2,myFilter3,myTree3);


Optimize (paramValues, theSplitLikFun);
lnLik1 = paramValues[1][0];
npar1 = paramValues[1][1]+9;