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/* This is an example HY-PHY Batch File.
It reads in a '#' nucleotide dataset data/hiv.nuc and estimates
maximum ln-likelihood based on the tree contained in the data file,
using Jukes Cantor 69 model.
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 nucleotideSequences = ReadDataFile ("data/hiv.nuc");
/* 2. Filter the data, specifying that all of the data is to be used
and that it is to be treated as nucleotides.*/
DataSetFilter filteredData = CreateFilter (nucleotideSequences,1);
/* 3. Define the F81 substitution matrix. '*' is defined to be -(sum of off-diag row elements) */
JC69RateMatrix =
{{*,mu,mu,mu}
{mu,*,mu,mu}
{mu,mu,*,mu}
{mu,mu,mu,*}};
/*4. Define the F81 models, by combining the substitution matrix with the vector of equal equilibrim
frequencies. */
equalFreqs = {{.25}{.25}{.25}{.25}};
Model F81 = (JC69RateMatrix, equalFreqs);
/*5. Now we can define the tree variable, using the tree string read from the data file,
and, by default, assigning the last defined model (JC69) to all tree branches. */
Tree givenTree = 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, givenTree);
/*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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