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#include <fstream>
#include <iostream>
#include <string>
#include <iomanip>
using namespace std;
#include "nucJC.h"
#include "sequence.h"
#include "distribution.h"
#include "stochasticProcess.h"
#include "gammaDistribution.h"
#include "uniDistribution.h"
#include "trivialAccelerator.h"
#include "sequenceContainer.h"
#include "nucleotide.h"
#include "phylipFormat.h"
#include "likelihoodComputation.h"
#include "bestHKYparam.h"
#include "evaluateCharacterFreq.h"
#include "bblEM.h"
#include "allTrees.h"
int main(int argc,char*argv []) {
cout<<"exhaustive search"<<endl;
// getting the data.
string seqFile1 = "nuc7.phylip.txt";
ifstream in1(seqFile1.c_str());
if (!in1) {errorMsg::reportError("unable to open input sequence file");}
nucleotide myAlph;
sequenceContainer original1 = phylipFormat::read(in1,&myAlph);
in1.close();
distribution *dist = new uniDistribution;
replacementModel *probMod=new nucJC;
pijAccelerator * pijAcc = new trivialAccelerator(probMod);
stochasticProcess sp(dist, pijAcc);
allTrees allTrees1(false);
allTrees1.recursiveFind(&original1,&sp);
cout<<" Log likelihood for best tree = "<<allTrees1.getBestScore()<<endl;
allTrees1.getBestTree().output(cout);
delete dist;
delete probMod;
return 0;
}
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