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fastcodeml

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    Cleaning
    mvalle authored 
    Added better support for XMT


git-svn-id: https://svn.vital-it.ch/svn/hp2c/trunk/Codeml_Variants/Fastcodeml@5019 95c5a404-1f88-0410-a6b0-c3f062b6f34a
    c34560cb
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    user avatar c34560cb
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    Name Last commit Last update
    simpleopt
    AlignedAllocator.cpp
    AlignedAllocator.h
    AlignedMalloc.h
    BayesTest.cpp
    BayesTest.h
    BranchSiteModel.cpp
    BranchSiteModel.h
    CMakeLists.txt
    CmdLine.cpp
    CmdLine.h
    CodeMLoptimizer.cpp
    CodeMLoptimizer.h
    CodonFrequencies.cpp
    CodonFrequencies.h
    CompilerHints.h
    DAGScheduler.cpp
    DAGScheduler.h
    Doxyfile
    Exceptions.h
    FatVectorTransform.cpp
    FatVectorTransform.h
    FillMatrix.cpp
    Forest.cpp
    Forest.h
    ForestExport.cpp
    ForestExport.h
    ForestNode.h
    Genes.cpp
    Genes.h
    HighLevelCoordinator.cpp
    HighLevelCoordinator.h
    INSTALL_CASTOR_MPI
    INSTALL_CASTOR_SEQ
    INSTALL_DEVCPT03
    INSTALL_EEEPC
    INSTALL_MACBOOK
    INSTALL_MACPRO
    MathSupport.h
    MatrixSize.h
    Newick.cpp
    Newick.h
    NewickGrammar.h
    ParseParameters.cpp
    ParseParameters.h
    Phylip.cpp
    Phylip.h
    PhyloTree.cpp
    PhyloTree.h
    ProbabilityMatrixSet.cpp
    ProbabilityMatrixSet.h
    README
    Timer.h
    TransitionMatrix.cpp
    TransitionMatrix.h
    TreeAndSetsDependencies.cpp
    TreeAndSetsDependencies.h
    TreeNode.cpp
    TreeNode.h
    Types.h
    VerbosityLevels.cpp
    VerbosityLevels.h
    WriteResults.cpp
    WriteResults.h
    blas.h
    fast.cpp
    fast.supp
    genQ.r
    lapack.h
    run.bat
    run.sh
    README
    How to compile without CMake:
g++ *.cpp ./libblas.a ./liblapack.a ./libblas.a ./liblapack.a ./libnlopt.a -DUSE_LAPACK -D_USE_OPTIMIZER -lgfortran -lm -o codeml
Notice this does NOT optimize the code!!!