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/* This is an example HY-PHY Batch File.
This file contains the shared part of "ReplicateConstraint" examples.
Sergei L. Kosakovsky Pond and Spencer V. Muse
June 2001.
*/
/* 1. Read in the data and store the result in a DataSet variable.*/
DataSet nucleotideSequences = ReadDataFile ("data/hiv.seq");
/* 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. Collect observed nucleotide frequencies from the filtered data. observedFreqs will
store the vector of frequencies. */
HarvestFrequencies (observedFreqs, filteredData, 1, 1, 1);
/* 4. Define the HKY substitution matrix. '*' is defined to be -(sum of off-diag row elements) */
HKY85RateMatrix =
{{*,trvs,trst,trvs}
{trvs,*,trvs,trst}
{trst,trvs,*,trvs}
{trvs,trst,trvs,*}};
/*5. Define the HKY85 model, by combining the substitution matrix with the vector of observed (equilibrium)
frequencies. */
Model HKY85 = (HKY85RateMatrix , observedFreqs);
/*6. Use the tree from the data file:
(((317,6767),((135,(529,105r))iNode1,(719,136))),6760,((113,9939),(256,(822,159))iNode2))
*/
Tree hivTree = DATAFILE_TREE;
/*7. Since all the likelihood function ingredients (data, tree, equilibrium frequencies)
have been defined we are ready to construct the likelihood function. */
LikelihoodFunction hivLik = (filteredData, hivTree);
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