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/* This is an example HY-PHY Batch File.
It reads in a PHYLIP amino-acid dataset data/stewart.aa and estimates
maximum ln-likelihood based on the tree contained in the data file,
using Equal Input (proportional) model for amino-acids.
Output is printed out as a Newick Style tree with branch lengths
representing the number of expected substitutions per branch (which
is the default setting for nucleotide models w/o rate variation).
Sergei L. Kosakovsky Pond and Spencer V. Muse
December 1999.
*/
/* 1. Read in the data and store the result in a DataSet variable.*/
DataSet aaSequences = ReadDataFile ("data/stewart.aa");
/* 2. Filter the data, specifying that all of the data is to be used
and that it is to be treated as amino-acids.*/
DataSetFilter filteredData = CreateFilter (aaSequences,1);
/* 3. Collect observed frequencies from the filtered data. observedFreq will store the vector of amino-acid frequencies. */
HarvestFrequencies (observedFreqs, filteredData, 1, 1, 1);
/* 4. Defines the rate matrix for the equal input model. */
EEAA = {20,20}; /* Create an empty 20x20 matrix named EEAA */
for (i=0; i<19;i=i+1)
{
for (j=i+1; j<20; j=j+1)
{
EEAA[i][j]:=a;
EEAA[j][i]:=a;
}
}
Model EqualInputModel = (EEAA, observedFreqs);
/*5. Define the tree variable, using the tree from the data */
Tree theTree = DATAFILE_TREE;
/*6. Since all the likelihood function ingredients (data, tree, equilibrium frequencies) have been defined we are ready to construct the likelihood function. */
LikelihoodFunction theLnLik = (filteredData, theTree);
/*7. Maximize the likelihood function, storing parameter values in the matrix paramValues */
Optimize (paramValues, theLnLik);
/*8. Print the tree with optimal branch lengths to the console. */
fprintf (stdout, theLnLik);
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