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/* This is an example HY-PHY Batch File.
It reads in a '#' nucleotide dataset data/molclock.seq and performs
a series of molecular clock tests on the data using the F81 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).
Also, the likelihood ratio statistic is evaluated and the P-values
for the tests are reported.
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/molclock.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);
F81RateMatrix =
{{*,mu,mu,mu}
{mu,*,mu,mu}
{mu,mu,*,mu}
{mu,mu,mu,*}};
/*5. Define the F81 models, by combining the substitution matrix with the vector of observed
(equilibrium) frequencies. We define one for each block, since the equilibrium
frequencies will differ. */
Model F81 = (F81RateMatrix, observedFreqs);
/*6. Now we can define the tree for the data just read taxa. Notice that
some of the internal nodes are named for later use.*/
Tree theTree = (TAAJ153,(HVRNASS,(RICRSS3,((ZMSUCS1,(OSRSS1A,(TASUCSYN1,HVSSYNMR)Internal1)),(MZESUS1,ORRSS2)Internal2))));
/*7. 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);
/*8. Maximize the likelihood function, storing parameter values in the matrix paramValues.
We also store the resulting ln-lik and the number of model parameters. */
Optimize (paramValues, theLnLik);
unconstrainedLnLik = paramValues[1][0];
paramCount = paramValues[1][1];
/*9. Print the tree with optimal branch lengths to the console. */
fprintf (stdout, "\n 0).UNCONSTRAINED MODEL:", theLnLik);
/*10. Now we impose the molecular clock constraint on the entire tree,
enforcing the clock on parameter mu.*/
MolecularClock (theTree, mu);
/*11. We maximize the tree with molecular clock constraints and report the results.*/
Optimize (paramValues, theLnLik);
lnlikDelta = 2 (unconstrainedLnLik-paramValues[1][0]);
pValue = 1-CChi2 (lnlikDelta, paramCount - paramValues[1][1]);
fprintf (stdout, "\n\n1). Global Molecular Clock; the P-value is:", pValue, "\n", theLnLik);
/*12. We can now try to impose molecular clock only on a subtree of the original tree.
First we do that for the subtree starting at the node Internal1 */
ClearConstraints (theTree);
MolecularClock (theTree.Internal1, mu);
Optimize (paramValues, theLnLik);
lnlikDelta = 2 (unconstrainedLnLik-paramValues[1][0]);
pValue = 1-CChi2 (lnlikDelta, paramCount - paramValues[1][1]);
fprintf (stdout, "\n\n2). Molecular Clock starting at Internal1; the P-value is:", pValue, "\n", theLnLik);
/*12. Secondly, we apply the clock for the subtree starting at the node Internal2,
in addition to the clock imposed in Step 11. */
MolecularClock (theTree.Internal2, mu);
Optimize (paramValues, theLnLik);
lnlikDelta = 2 (unconstrainedLnLik-paramValues[1][0]);
pValue = 1-CChi2 (lnlikDelta, paramCount - paramValues[1][1]);
fprintf (stdout, "\n\n3). Molecular Clock starting at Internal1 and Internal2; the P-value is:", pValue, "\n", theLnLik);
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