/usr/include/Bpp/Phyl/Likelihood.all is in libbpp-phyl-dev 2.0.3-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 | #include "Likelihood/AbstractDiscreteRatesAcrossSitesTreeLikelihood.h"
#include "Likelihood/AbstractHomogeneousTreeLikelihood.h"
#include "Likelihood/AbstractNonHomogeneousTreeLikelihood.h"
#include "Likelihood/AbstractTreeLikelihood.h"
#include "Likelihood/AbstractTreeLikelihoodData.h"
#include "Likelihood/ClockTreeLikelihood.h"
#include "Likelihood/DRASDRTreeLikelihoodData.h"
#include "Likelihood/DRASRTreeLikelihoodData.h"
#include "Likelihood/DRHomogeneousMixedTreeLikelihood.h"
#include "Likelihood/DRHomogeneousTreeLikelihood.h"
#include "Likelihood/DRNonHomogeneousTreeLikelihood.h"
#include "Likelihood/DRTreeLikelihood.h"
#include "Likelihood/DRTreeLikelihoodTools.h"
#include "Likelihood/DiscreteRatesAcrossSitesTreeLikelihood.h"
#include "Likelihood/GlobalClockTreeLikelihoodFunctionWrapper.h"
#include "Likelihood/HomogeneousTreeLikelihood.h"
#include "Likelihood/MarginalAncestralStateReconstruction.h"
#include "Likelihood/NNIHomogeneousTreeLikelihood.h"
#include "Likelihood/NonHomogeneousTreeLikelihood.h"
#include "Likelihood/PairedSiteLikelihoods.h"
#include "Likelihood/PseudoNewtonOptimizer.h"
#include "Likelihood/RASTools.h"
#include "Likelihood/RHomogeneousClockTreeLikelihood.h"
#include "Likelihood/RHomogeneousMixedTreeLikelihood.h"
#include "Likelihood/RHomogeneousTreeLikelihood.h"
#include "Likelihood/RNonHomogeneousMixedTreeLikelihood.h"
#include "Likelihood/RNonHomogeneousTreeLikelihood.h"
#include "Likelihood/SitePartitionTreeLikelihood.h"
#include "Likelihood/TreeLikelihood.h"
#include "Likelihood/TreeLikelihoodData.h"
#include "Likelihood/TreeLikelihoodTools.h"
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