ML_util.h

#include "ALE.h"

// From the STL:
#include <iostream>
#include <iomanip>
#include <limits>


#include <Bpp/Numeric/Prob/DiscreteDistribution.h>
#include <Bpp/Numeric/Prob/ConstantDistribution.h>
#include <Bpp/Numeric/DataTable.h>
#include <Bpp/Numeric/Matrix/MatrixTools.h>
#include <Bpp/Numeric/VectorTools.h>
#include <Bpp/Numeric/AutoParameter.h>
#include <Bpp/App/BppApplication.h>
#include <Bpp/App/ApplicationTools.h>
#include <Bpp/Io/FileTools.h>
#include <Bpp/Text/TextTools.h>
#include <Bpp/Text/KeyvalTools.h>

// From SeqLib:
#include <Bpp/Seq/Alphabet/Alphabet.h>
#include <Bpp/Seq/Container/VectorSiteContainer.h>
#include <Bpp/Seq/SiteTools.h>
#include <Bpp/Seq/App/SequenceApplicationTools.h>
#include <Bpp/Seq/Io.all>

// From PhylLib:
#include <Bpp/Phyl/Tree.h>
#include <Bpp/Phyl/Likelihood.all>
#include <Bpp/Phyl/PatternTools.h>
#include <Bpp/Phyl/App/PhylogeneticsApplicationTools.h>
#include <Bpp/Phyl/OptimizationTools.h>
#include <Bpp/Phyl/Model.all>
#include <Bpp/Phyl/Io/Newick.h>
#include <Bpp/Phyl/Mapping.all>

scalar_type tree_LL(std::string tree,std::string aln_fname,bool optimize_bls=true,scalar_type tolerance=1e-1);
std::pair<string,scalar_type> tree_LL_nucl(std::string tree,std::string aln_fname,bool optimize_bls=true,scalar_type tolerance=1e-1);

std::vector<std::string> all_NNIs(string Sstring,bool rooted=false);