#include <Bpp/App/ApplicationTools.h>
#include <Bpp/Io/OutputStream.h>
#include <Bpp/Numeric/Function/SimpleNewtonMultiDimensions.h>
#include <Bpp/Phyl/OptimizationTools.h>
#include "../Parsimony/DRTreeParsimonyScore.h"
#include "../Tree/TreeTemplate.h"
#include "Likelihood/NNIHomogeneousTreeLikelihood.h"
#include "Tree/NNITopologySearch.h"

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Classes
class	bpp::NNITopologyListener
	Listener used internally by the optimizeTreeNNI method. More...

class	bpp::NNITopologyListener2
	Listener used internally by the optimizeTreeNNI2 method. More...

class	bpp::LegacyOptimizationTools
	Optimization methods for phylogenetic inference. More...

class	bpp::LegacyOptimizationTools::ScaleFunction

Namespaces
	bpp
	Defines the basic types of data flow nodes.

Classes

Namespaces